Updated on 2025/06/06

写真b

 
YAMADA Yasuyuki
 
*Items subject to periodic update by Rikkyo University (The rest are reprinted from information registered on researchmap.)
Affiliation*
College of Science Department of Life Science
Graduate School of Science Doctoral Program in Life Science
Graduate School of Science Master's Program in Life Science
Title*
Professor
Degree
博士（理学） （ 3 1999   東京工業大学 ） / 修士（理学） （ 3 1996   東京工業大学 ）
Contact information
Mail Address
Research Interests

  • allosteric

  • regulation

  • ATP synthase

    • Campus Career*
    • 4 2015 - Present 
      College of Science   Department of Life Science   Professor
    • 4 2015 - Present 
      Graduate School of Science   Master's Program in Life Science   Professor
    • 4 2015 - Present 
      Graduate School of Science   Doctoral Program in Life Science   Professor
    • 4 2008 - 3 2015 
      College of Science   Department of Life Science   Associate Professor
    • 4 2008 - 3 2015 
      Graduate School of Science   Master's Program in Life Science   Associate Professor
    • 4 2008 - 3 2015 
      Graduate School of Science   Doctoral Program in Life Science   Associate Professor
    • 4 2004 - 3 2008 
      College of Science   Department of Life Science   Lecturer
    • 4 2005 - 3 2008 
      Graduate School of Science   Master's Program in Life Science   Lecturer
    • 4 2005 - 3 2008 
      Graduate School of Science   Doctoral Program in Life Science   Lecturer

    ▼display all

     

    Research Areas

    • Life Science / Biophysics

    • Life Science / Functional biochemistry

    Research History

    • 4 2015 - Present 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Professor

      ▶ More details

    • 4 2008 - 3 2015 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Associate Professor

      ▶ More details

    • 4 2004 - 3 2008 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Lecturer

      ▶ More details

    • 4 2003 - 3 2004 
      The University of Tokyo   Institute of Industrial Science

      ▶ More details

    • 4 1999 - 3 2003 
      日本学術振興会   特別研究員（PD）

      ▶ More details

    • 4 1998 - 3 1999 
      日本学術振興会   特別研究員（DC2)

      ▶ More details

    ▼display all

    Education

    • 4 1996 - 3 1999 
      Tokyo Institute of Technology   Graduate School, Division of Life Science and Engineering

      ▶ More details

      Country： Japan

      researchmap

    • 4 1994 - 3 1996 
      Tokyo Institute of Technology   Graduate School, Division of Life Science and Engineering

      ▶ More details

      Country： Japan

      researchmap

    • 4 1990 - 3 1994 
      Tokyo Institute of Technology   Faculty of Life Science and Engineering

      ▶ More details

      Country： Japan

      researchmap

    Awards

    • 10 2008  
      日本生化学会  平成２０年度 日本生化学会奨励賞 
       
      山田 康之

      ▶ More details

      Award type：Award from Japanese society, conference, symposium, etc.  Country：Japan

      researchmap

    Papers

    • Evolution of Ribosomal Protein S14 Demonstrated by the Reconstruction of Chimeric Ribosomes in Bacillus subtilis. Peer-reviewed International journal

      Genki Akanuma, Fujio Kawamura, Satoru Watanabe, Masaki Watanabe, Fumiya Okawa, Yousuke Natori, Hideaki Nanamiya, Kei Asai, Taku Chibazakura, Hirofumi Yoshikawa, Akiko Soma, Takashi Hishida, Yasuyuki Kato-Yamada

      Journal of bacteriology203 ( 10 )   21 4 2021

      ▶ More details

      Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

      Ribosomal protein S14 can be classified into three types. The first, the C+ type has a Zn2+ binding motif and is ancestral. The second and third are the C- short and C- long types, neither of which contain a Zn2+ binding motif and which are ca. 90 residues and 100 residues in length, respectively. In the present study, the C+ type S14 from Bacillus subtilis ribosomes (S14BsC+) were completely replaced by the heterologous C- long type of S14 from Escherichia coli (S14Ec) or Synechococcus elongatus (S14Se). Surprisingly, S14Ec and S14Se were incorporated fully into 70S ribosomes in B. subtilis However, the growth rates as well as the sporulation efficiency of the mutants harboring heterologous S14 were significantly decreased. In these mutants, the polysome fraction was decreased and the 30S and 50S subunits accumulated unusually, indicating that cellular translational activity of these mutants was decreased. In vitro analysis showed a reduction in the translational activity of the 70S ribosome fraction purified from these mutants. The abundance of ribosomal proteins S2 and S3 in the 30S fraction in these mutants was reduced while that of S14 was not significantly decreased. It seems likely that binding of heterologous S14 changes the structure of the 30S subunit, which causes a decrease in the assembly efficiency of S2 and S3, which are located near the binding site of S14. Moreover, we found that S3 from S. elongatus cannot function in B. subtilis unless S14Se is present.IMPORTANCE S14, an essential ribosomal protein, may have evolved to adapt bacteria to zinc-limited environments by replacement of a zinc-binding motif with a zinc-independent sequence. It was expected that the bacterial ribosome would be tolerant to replacement of S14 because of the previous prediction that the spread of C- type S14 involved horizontal gene transfer. In this study, we completely replaced the C+ type of S14 in B. subtilis ribosome with the heterologous C- long type of S14 and characterized the resulting chimeric ribosomes. Our results suggest that the B. subtilis ribosome is permissive for the replacement of S14, but coevolution of S3 might be required to utilize the C- long type of S14 more effectively.

      DOI： 10.1128/JB.00599-20

      PubMed

      researchmap

    • ATP-binding affinity of the ε subunit of thermophilic F1-ATPase under label-free conditions. Peer-reviewed International journal

      Miria Fujiwara, Yasuyuki Kato-Yamada

      Biochemistry and biophysics reports21   100725 - 100725   3 2020

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      The ε subunits of several bacterial F1-ATPases bind ATP. ATP binding to the ε subunit has been shown to be involved in the regulation of F1-ATPase from thermophilic Bacillus sp. PS3 (TF1). We previously reported that the dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C is 4.3 μM by measuring changes in the fluorescence of the dye attached to the ε subunit (Kato, S. et al. (2007) J. Biol. Chem. 282, 37618). However, we have recently noticed that this varies with the dye used. In this report, to determine the affinity for ATP under label-free conditions, we have measured the competitive displacement of 2'(3')-O-N'-methylaniloyl-aminoadenosine-5'-triphosphate (Mant-ATP), a fluorescent analog of ATP, by ATP. The dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C was determined to be 0.29 μM, which is one order of magnitude higher affinity than previously reported values.

      DOI： 10.1016/j.bbrep.2020.100725

      PubMed

      researchmap

    • C-terminal regulatory domain of the ε subunit of Fo F1 ATP synthase enhances the ATP-dependent H+ pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. Peer-reviewed International journal

      Genki Akanuma, Tomoaki Tagana, Maho Sawada, Shota Suzuki, Tomohiro Shimada, Kan Tanaka, Fujio Kawamura, Yasuyuki Kato-Yamada

      MicrobiologyOpen8 ( 8 ) e00815   8 2019

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      The ε subunit of Fo F1 -ATPase/synthase (Fo F1 ) plays a crucial role in regulating Fo F1 activity. To understand the physiological significance of the ε subunit-mediated regulation of Fo F1 in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C-terminal regulatory domain of the ε subunit (ε∆C ). Analyses using inverted membrane vesicles revealed that the ε∆C mutation decreased ATPase activity and the ATP-dependent H+ -pumping activity of Fo F1 . To enhance the effects of ε∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε∆C mutant strain). Interestingly, growth of the ∆rrn8 ε∆C mutant stalled at late-exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C-terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP-dependent H+ -pumping activity of Fo F1 .

      DOI： 10.1002/mbo3.815

      PubMed

      researchmap

    • Magnesium Suppresses Defects in the Formation of 70S Ribosomes as Well as in Sporulation Caused by Lack of Several Individual Ribosomal Proteins. Peer-reviewed International journal

      Genki Akanuma, Kotaro Yamazaki, Yuma Yagishi, Yuka Iizuka, Morio Ishizuka, Fujio Kawamura, Yasuyuki Kato-Yamada

      Journal of bacteriology200 ( 18 )   15 9 2018

      ▶ More details

      Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

      Individually, the ribosomal proteins L1, L23, L36, and S6 are not essential for cell proliferation of Bacillus subtilis, but the absence of any one of these ribosomal proteins causes a defect in the formation of the 70S ribosomes and a reduced growth rate. In mutant strains individually lacking these ribosomal proteins, the cellular Mg2+ content was significantly reduced. The deletion of YhdP, an exporter of Mg2+, and overexpression of MgtE, the main importer of Mg2+, increased the cellular Mg2+ content and restored the formation of 70S ribosomes in these mutants. The increase in the cellular Mg2+ content improved the growth rate and the cellular translational activity of the ΔrplA (L1) and the ΔrplW (L23) mutants but did not restore those of the ΔrpmJ (L36) and the ΔrpsF (S6) mutants. The lack of L1 caused a decrease in the production of Spo0A, the master regulator of sporulation, resulting in a decreased sporulation frequency. However, deletion of yhdP and overexpression of mgtE increased the production of Spo0A and partially restored the sporulation frequency in the ΔrplA (L1) mutant. These results indicate that Mg2+ can partly complement the function of several ribosomal proteins, probably by stabilizing the conformation of the ribosome.IMPORTANCE We previously reported that an increase in cellular Mg2+ content can suppress defects in 70S ribosome formation and growth rate caused by the absence of ribosomal protein L34. In the present study, we demonstrated that, even in mutants lacking individual ribosomal proteins other than L34 (L1, L23, L36, and S6), an increase in the cellular Mg2+ content could restore 70S ribosome formation. Moreover, the defect in sporulation caused by the absence of L1 was also suppressed by an increase in the cellular Mg2+ content. These findings indicate that at least part of the function of these ribosomal proteins can be complemented by Mg2+, which is essential for all living cells.

      DOI： 10.1128/JB.00212-18

      PubMed

      researchmap

    • Mechanistic Insights into the Activation of Soluble Guanylate Cyclase by Carbon Monoxide: A Multistep Mechanism Proposed for the BAY 41-2272 Induced Formation of 5-Coordinate CO-Heme. Peer-reviewed International journal

      Ryu Makino, Yuji Obata, Motonari Tsubaki, Tetsutaro Iizuka, Yuki Hamajima, Yasuyuki Kato-Yamada, Keisuke Mashima, Yoshitsugu Shiro

      Biochemistry57 ( 10 ) 1620 - 1631   13 3 2018

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      Soluble guanylate cyclase (sGC) is a heme-containing enzyme that catalyzes cGMP production upon sensing NO. While the CO adduct, sGC-CO, is much less active, the allosteric regulator BAY 41-2272 stimulates the cGMP productivity to the same extent as that of sGC-NO. The stimulatory effect has been thought to be likely associated with Fe-His bond cleavage leading to 5-coordinate CO-heme, but the detailed mechanism remains unresolved. In this study, we examined the mechanism under the condition including BAY 41-2272, 2'-deoxy-3'-GMP and foscarnet. The addition of these effectors caused the original 6-coordinate CO-heme to convert to an end product that was an equimolar mixture of a 5- and a new 6-coordinate CO-heme, as assessed by IR spectral measurements. The two types of CO-hemes in the end product were further confirmed by CO dissociation kinetics. Stopped-flow measurements under the condition indicated that the ferrous sGC bound CO as two reversible steps, where the primary step was assigned to the full conversion of the ferrous enzyme to the 6-coordinate CO-heme, and subsequently followed by the slower second step leading a partial conversion of the 6-coordinate CO-heme to the 5-coordinate CO-heme. The observed rates for both steps linearly depended on CO concentrations. The unexpected CO dependence of the rates in the second step supports a multistep mechanism, in which the 5-coordinate CO-heme is led by CO release from a putative bis-carbonyl intermediate that is likely provided by the binding of a second CO to the 6-coordinate CO-heme. This mechanism provides a new aspect on the activation of sGC by CO.

      DOI： 10.1021/acs.biochem.7b01240

      PubMed

      researchmap

    • Essential Role of the ε Subunit for Reversible Chemo-Mechanical Coupling in F1-ATPase. Peer-reviewed International journal

      Rikiya Watanabe, Makoto Genda, Yasuyuki Kato-Yamada, Hiroyuki Noji

      Biophysical journal114 ( 1 ) 178 - 187   9 1 2018

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      F1-ATPase is a rotary motor protein driven by ATP hydrolysis. Among molecular motors, F1 exhibits unique high reversibility in chemo-mechanical coupling, synthesizing ATP from ADP and inorganic phosphate upon forcible rotor reversal. The ε subunit enhances ATP synthesis coupling efficiency to > 70% upon rotation reversal. However, the detailed mechanism has remained elusive. In this study, we performed stall-and-release experiments to elucidate how the ε subunit modulates ATP association/dissociation and hydrolysis/synthesis process kinetics and thermodynamics, key reaction steps for efficient ATP synthesis. The ε subunit significantly accelerated the rates of ATP dissociation and synthesis by two- to fivefold, whereas those of ATP binding and hydrolysis were not enhanced. Numerical analysis based on the determined kinetic parameters quantitatively reproduced previous findings of two- to fivefold coupling efficiency improvement by the ε subunit at the condition exhibiting the maximum ATP synthesis activity, a physiological role of F1-ATPase. Furthermore, fundamentally similar results were obtained upon ε subunit C-terminal domain truncation, suggesting that the N-terminal domain is responsible for the rate enhancement.

      DOI： 10.1016/j.bpj.2017.11.004

      PubMed

      researchmap

    • The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase. Peer-reviewed International journal

      Alexander Krah, Yasuyuki Kato-Yamada, Shoji Takada

      PloS one12 ( 5 ) e0177907   2017

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1371/journal.pone.0177907

      PubMed

      researchmap

    • Pressure adaptation of 3-isopropylmalate dehydrogenase from an extremely piezophilic bacterium is attributed to a single amino acid substitution. Peer-reviewed International journal

      Yuki Hamajima, Takayuki Nagae, Nobuhisa Watanabe, Eiji Ohmae, Yasuyuki Kato-Yamada, Chiaki Kato

      Extremophiles : life under extreme conditions20 ( 2 ) 177 - 86   3 2016

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1007/s00792-016-0811-4

      PubMed

      researchmap

    • Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis. Peer-reviewed International journal

      Genki Akanuma, Yuka Kazo, Kazumi Tagami, Hirona Hiraoka, Koichi Yano, Shota Suzuki, Ryo Hanai, Hideaki Nanamiya, Yasuyuki Kato-Yamada, Fujio Kawamura

      Microbiology (Reading, England)162 ( 3 ) 448 - 458   3 2016

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1099/mic.0.000234

      PubMed

      researchmap

    • High affinity nucleotide-binding mutant of the ε subunit of thermophilic F1-ATPase. Peer-reviewed International journal

      Yasuyuki Kato-Yamada

      Biochemical and biophysical research communications469 ( 4 ) 1129 - 32   22 1 2016

      ▶ More details

      Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1016/j.bbrc.2015.12.121

      PubMed

      researchmap

    • Pressure effects on the chimeric 3-isopropylmalate dehydrogenases of the deep-sea piezophilic Shewanella benthica and the atmospheric pressure-adapted Shewanella oneidensis. Peer-reviewed International journal

      Yuki Hamajima, Takayuki Nagae, Nobuhisa Watanabe, Yasuyuki Kato-Yamada, Takeo Imai, Chiaki Kato

      Bioscience, biotechnology, and biochemistry78 ( 3 ) 469 - 71   2014

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1080/09168451.2014.890033

      PubMed

      researchmap

    • Severe MgADP inhibition of Bacillus subtilis F1-ATPase is not due to the absence of nucleotide binding to the noncatalytic nucleotide binding sites. Peer-reviewed International journal

      Toru Ishikawa, Yasuyuki Kato-Yamada

      PloS one9 ( 9 ) e107197   2014

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1371/journal.pone.0107197

      PubMed

      researchmap

    • ε subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition. Peer-reviewed International journal

      Junya Mizumoto, Yuka Kikuchi, Yo-Hei Nakanishi, Naoto Mouri, Anrong Cai, Tokushiro Ohta, Takamitsu Haruyama, Yasuyuki Kato-Yamada

      PloS one8 ( 8 ) e73888   2013

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Public Library of Science  

      DOI： 10.1371/journal.pone.0073888

      Scopus

      PubMed

      researchmap

    • Hydrophobic shield on the molecular surface enhances thermal stability of ferredoxin of Cyanidioschyzon merolae Peer-reviewed

      Yuko Ueno, Yasuyuki Kato-Yamada, Takeo Imai

      Journal of Japanese Society for Extremophiles11 ( 2 ) 59 - 63   2012

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      CiNii Article

      researchmap

    • ATP binding to the ϵ subunit of thermophilic ATP synthase is crucial for efficient coupling of ATPase and H+ pump activities. Peer-reviewed International journal

      Fumitaka Kadoya, Shigeyuki Kato, Kei Watanabe, Yasuyuki Kato-Yamada

      The Biochemical journal437 ( 1 ) 135 - 40   1 7 2011

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1042/BJ20110443

      PubMed

      researchmap

    • Conformational transitions of subunit epsilon in ATP synthase from thermophilic Bacillus PS3. Peer-reviewed International journal

      Boris A Feniouk, Yasuyuki Kato-Yamada, Masasuke Yoshida, Toshiharu Suzuki

      Biophysical journal98 ( 3 ) 434 - 42   3 2 2010

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1016/j.bpj.2009.10.023

      PubMed

      researchmap

    • Inhibition of thermophilic F1-ATPase by the ε subunit takes different path from the ADP-Mg inhibition. Peer-reviewed

      Takamitsu Haruyama, Yoko Hirono-Hara, Yasuyuki Kato-Yamada

      Biophysics (Nagoya-shi, Japan)6   59 - 65   2010

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.2142/biophysics.6.59

      Scopus

      PubMed

      researchmap

    • Modulation of nucleotide binding to the catalytic sites of thermophilic F(1)-ATPase by the epsilon subunit: implication for the role of the epsilon subunit in ATP synthesis. Peer-reviewed International journal

      Taichi Yasuno, Eiro Muneyuki, Masasuke Yoshida, Yasuyuki Kato-Yamada

      Biochemical and biophysical research communications390 ( 2 ) 230 - 4   11 12 2009

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1016/j.bbrc.2009.09.092

      PubMed

      researchmap

    • Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Peer-reviewed International journal

      Hiromi Imamura, Kim P Huynh Nhat, Hiroko Togawa, Kenta Saito, Ryota Iino, Yasuyuki Kato-Yamada, Takeharu Nagai, Hiroyuki Noji

      Proceedings of the National Academy of Sciences of the United States of America106 ( 37 ) 15651 - 6   15 9 2009

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1073/pnas.0904764106

      PubMed

      researchmap

    • Role of the epsilon subunit of thermophilic F1-ATPase as a sensor for ATP. Peer-reviewed International journal

      Shigeyuki Kato, Masasuke Yoshida, Yasuyuki Kato-Yamada

      The Journal of biological chemistry282 ( 52 ) 37618 - 23   28 12 2007

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      PubMed

      researchmap

    • Structures of the thermophilic F1-ATPase epsilon subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1. Peer-reviewed International journal

      Hiromasa Yagi, Nobumoto Kajiwara, Hideaki Tanaka, Tomitake Tsukihara, Yasuyuki Kato-Yamada, Masasuke Yoshida, Hideo Akutsu

      Proceedings of the National Academy of Sciences of the United States of America104 ( 27 ) 11233 - 8   3 7 2007

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      The epsilon subunit of bacterial and chloroplast F(o)F(1)-ATP synthases modulates their ATP hydrolysis activity. Here, we report the crystal structure of the ATP-bound epsilon subunit from a thermophilic Bacillus PS3 at 1.9-A resolution. The C-terminal two alpha-helices were folded into a hairpin, sitting on the beta sandwich structure, as reported for Escherichia coli. A previously undescribed ATP binding motif, I(L)DXXRA, recognizes ATP together with three arginine and one glutamate residues. The E. coli epsilon subunit binds ATP in a similar manner, as judged on NMR. We also determined solution structures of the C-terminal domain of the PS3 epsilon subunit and relaxation parameters of the whole molecule by NMR. The two helices fold into a hairpin in the presence of ATP but extend in the absence of ATP. The latter structure has more helical regions and is much more flexible than the former. These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase.

      PubMed

      researchmap

    • 3P170 Single molecule dynamics of the epsilon subunit in F_1 forced-rotated by magnetic tweezers(Molecular motors,Oral Presentations)

      Saita Eiichiro, Iino Ryota, Yamada-Kato Yasuyuki, Suzuki Toshiharu, Noji Hiroyuki, Yoshida Maasuke

      Seibutsu Butsuri47   S245   2007

      ▶ More details

      Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.47.S245_3

      CiNii Article

      researchmap

    • gammaepsilon Sub-complex of thermophilic ATP synthase has the ability to bind ATP. Peer-reviewed International journal

      Satoshi Iizuka, Shigeyuki Kato, Masasuke Yoshida, Yasuyuki Kato-Yamada

      Biochemical and biophysical research communications349 ( 4 ) 1368 - 71   3 11 2006

      ▶ More details

      Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1016/j.bbrc.2006.09.001

      PubMed

      researchmap

    • 1P301 ε Subunit Stops Rotation of Thermophilic F1-ATPase; Single Molecular Analysis of the inhibition by the ε subunit(9. Molecular motor (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

      Haruyama Takamitsu, Hirono-Hara Yoko, Noji Hiroyuki, Kato-Yamada Yasuyuki

      Seibutsu Butsuri46 ( 2 ) S222   2006

      ▶ More details

      Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.46.S222_1

      CiNii Article

      researchmap

    • Isolated epsilon subunit of Bacillus subtilis F1-ATPase binds ATP. Peer-reviewed International journal

      Yasuyuki Kato-Yamada

      FEBS letters579 ( 30 ) 6875 - 8   19 12 2005

      ▶ More details

      Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1016/j.febslet.2005.11.036

      PubMed

      researchmap

    • Real-time monitoring of conformational dynamics of the epsilon subunit in F1-ATPase. Peer-reviewed International journal

      Ryota Iino, Tomoe Murakami, Satoshi Iizuka, Yasuyuki Kato-Yamada, Toshiharu Suzuki, Masasuke Yoshida

      The Journal of biological chemistry280 ( 48 ) 40130 - 4   2 12 2005

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1074/jbc.M506160200

      PubMed

      researchmap

    • Highly coupled ATP synthesis by F1-ATPase single molecules. Peer-reviewed International journal

      Yannick Rondelez, Guillaume Tresset, Takako Nakashima, Yasuyuki Kato-Yamada, Hiroyuki Fujita, Shoji Takeuchi, Hiroyuki Noji

      Nature433 ( 7027 ) 773 - 7   17 2 2005

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1038/nature03277

      PubMed

      researchmap

    • 3P164 Confomations of epsilon subunit in F_1 forced-rotated by magnetic tweezers

      Saita E., Iino R., Kato-Yamada Y., Noji H., Suzuki T., Yoshida M.

      Seibutsu Butsuri45   S244   2005

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.45.S244_4

      CiNii Article

      researchmap

    • 2P175 Forced rotation of F_1-ATPase in forward directoin enhances ATP hydrolysis

      Nakashima T., RONDELEZ Yannick, Tresset Guillaume, Yamada Y., Sakakihara S., Fujita H., Takeuchi S., Noji H.

      Seibutsu Butsuri45   S163   2005

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.45.S163_3

      CiNii Article

      researchmap

    • 3P021 Induction factor of structure chnage of TF_1 epsilon subunit

      Yagi H., Kajiwara N., Tanaka H., Tsukihara T., Yamada Y., Yoshida M., Akutsu H.

      Seibutsu Butsuri45   S209   2005

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.45.S209_1

      CiNii Article

      researchmap

    • 1P151 Development and verification of the observation system for F_oF_1-ATP synthase rotation driven by membrane potential

      Tabata K., Iino R., Ueno H., Yamada-Kato Y., Ide T., Noji H.

      Seibutsu Butsuri45   S69   2005

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.45.S69_3

      CiNii Article

      researchmap

    • Winding up single F-I-motor protein in femtoliter chambers: The molecular pull-back car. Peer-reviewed

      Y Rondelez, G Tresset, Y Kato-Yamada, H Fujita, S Takeuchi, H Noji

      Micro Total Analysis Systems 2004, Vol 1 ( 296 ) 21 - 23   2005

      ▶ More details

      Language：English   Publishing type：Research paper (international conference proceedings)  

      researchmap

    • Planar lipid bilayer chip for electrophysiological analysis of membrane proteins Peer-reviewed

      H Suzuki, K Tabata, Y Kato-Yamada, H Noji, S Takeuchi

      MICRO TOTAL ANALYSIS SYSTEMS 2004, VOL 2 ( 297 ) 246 - 248   2005

      ▶ More details

      Language：English   Publishing type：Research paper (international conference proceedings)  

      researchmap

    • Ultra-small chamber for single-molecule detection of biological reaction

      Hiroyuki Noji, Yannick Rondelez, Takako Nakashima, Guillaume Tresset, Kazuhito Tabata, Yasuyuki Kato-Yamada, Hiroyuki Fujita, Shoji Takeuchi

      e-Journal of Surface Science and Nanotechnology3   79 - 81   2005

      ▶ More details

      Publishing type：Research paper (scientific journal)   Publisher：Surface Science Society Japan  

      DOI： 10.1380/ejssnt.2005.79

      researchmap

    • Planar lipid bilayer reconstitution with a micro-fluidic system. International journal

      Hiroaki Suzuki, Kazuhito Tabata, Yasuyuki Kato-Yamada, Hiroyuki Noji, Shoji Takeuchi

      Lab on a chip4 ( 5 ) 502 - 5   10 2004

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      A planar lipid bilayer which is widely used for the electrophysiological study of membrane proteins in laboratories is reconstituted using a micro-fluidic system, in a manner that is suitable for automated processing. We fabricated micro-channels on both sides of the substrate, which are connected through a 100-200 microm aperture, and showed that the bilayer can be formed at the aperture by flowing the lipid solution and buffer, alternately. Parylene coating is found to be suitable for both bilayer formation and electric noise reduction. Future applications include a high-sensitivity ion sensor chip and a high-throughput drug screening device.

      PubMed

      researchmap

    • Planar lipid membrane array for membrane protein chip Peer-reviewed

      H Suzuki, Y Kato-Yamada, H Noji, S Takeuchi

      MEMS 2004: 17TH IEEE INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, TECHNICAL DIGEST   272 - 275   2004

      ▶ More details

      Language：English   Publishing type：Research paper (international conference proceedings)  

      researchmap

    • 3P143 Highly coupled ATP synthesis by single Fl molecule

      Rondelez Yannick, Nakashima T., Tresset Guillaume, Yamada Y., Fujita H., Takeuchi S., Noji H.

      Seibutsu Butsuri44   S225   2004

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.44.S225_3

      CiNii Article

      researchmap

    • 3P137 X-ray crystal structure analysis of TF_1 epsilon subunit

      Kajiwara N., Tanaka H., Yagi H., Tsukihara T., Yamada Y., Yoshida M., Akutsu H.

      Seibutsu Butsuri44   S224   2004

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.44.S224_1

      CiNii Article

      researchmap

    • Planar lipid bilayer reconstitution with a micro-fluidic system Peer-reviewed

      H Suzuki, K Tabata, Y Kato-Yamada, H Noji, S Takeuchi

      LAB ON A CHIP4 ( 5 ) 502 - 505   2004

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      DOI： 10.1039/b405967k

      researchmap

    • Isolated epsilon subunit of thermophilic F1-ATPase binds ATP. Peer-reviewed International journal

      Yasuyuki Kato-Yamada, Masasuke Yoshida

      The Journal of biological chemistry278 ( 38 ) 36013 - 6   19 9 2003

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      F1-ATPase, a soluble part of the F0F1-ATP synthase, has subunit structure alpha3beta3gammadeltaepsilon in which nucleotide-binding sites are located in the alpha and beta subunits and, as believed, in none of the other subunits. However, we report here that the isolated epsilon subunit of F1-ATPase from thermophilic Bacillus strain PS3 can bind ATP. The binding was directly demonstrated by isolating the epsilon subunit-ATP complex with gel filtration chromatography. The binding was not dependent on Mg2+ but was highly specific for ATP; however, ADP, GTP, UTP, and CTP failed to bind. The epsilon subunit lacking the C-terminal helical hairpin was unable to bind ATP. Although ATP binding to the isolated epsilon subunits from other organisms has not been detected under the same conditions, a possibility emerges that the epsilon subunit acts as a built in cellular ATP level sensor of F0F1-ATP synthase.

      PubMed

      researchmap

    • The role of the beta DELSEED motif of F-1-ATPase - Propagation of the inhibitory effect of the epsilon subunit Peer-reviewed

      KY Hara, Y Kato-Yamada, Y Kikuchi, T Hisabori, M Yoshida

      JOURNAL OF BIOLOGICAL CHEMISTRY276 ( 26 ) 23969 - 23973   6 2001

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • The mechanism of ATPase regulation of F_1-ATPase

      Hara K.Y., Kato-Yamada Y., Hisabori T., Yoshida M.

      Seibutsu Butsuri41   S96   2001

      ▶ More details

      Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

      DOI： 10.2142/biophys.41.S96_2

      CiNii Article

      researchmap

    • Movement of the helical domain of the epsilon subunit is required for the activation of thermophilic F-1-ATPase Peer-reviewed

      Y Kato-Yamada, M Yoshida, T Hisabori

      JOURNAL OF BIOLOGICAL CHEMISTRY275 ( 46 ) 35746 - 35750   11 2000

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • epsilon Subunit, an endogenous inhibitor of bacterial F-1-ATPase, also inhibits F0F1-ATPase Peer-reviewed

      Y Kato-Yamada, D Bald, M Koike, K Motohashi, T Hisabori, M Yoshida

      JOURNAL OF BIOLOGICAL CHEMISTRY274 ( 48 ) 33991 - 33994   11 1999

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • Direct observation of the rotation of epsilon subunit in F-1-ATPase Peer-reviewed

      Y Kato-Yamada, H Noji, R Yasuda, K Kinosita, M Yoshida

      JOURNAL OF BIOLOGICAL CHEMISTRY273 ( 31 ) 19375 - 19377   7 1998

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • Thermophilic F-1-ATPase is activated without dissociation of an endogenous inhibitor, epsilon subunit Peer-reviewed

      Y Kato, T Matsui, N Tanaka, E Muneyuki, T Hisabori, M Yoshida

      JOURNAL OF BIOLOGICAL CHEMISTRY272 ( 40 ) 24906 - 24912   10 1997

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • The regulatory functions of the gamma and epsilon subunits from chloroplast CF1 are transferred to the core complex, alpha(3)beta(3), from thermophilic bacterial F-1 Peer-reviewed

      T Hisabori, Y Kato, K Motohashi, P KrothPancic, H Strotmann, T Amano

      EUROPEAN JOURNAL OF BIOCHEMISTRY247 ( 3 ) 1158 - 1165   8 1997

      ▶ More details

      Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    • ANALYSIS OF TIME-DEPENDENT CHANGE OF ESCHERICHIA-COLI F1-ATPASE ACTIVITY AND ITS RELATIONSHIP WITH APPARENT NEGATIVE COOPERATIVITY Peer-reviewed

      Y KATO, T SASAYAMA, E MUNEYUKI, M YOSHIDA

      BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS1231 ( 3 ) 275 - 281   10 1995

      ▶ More details

      Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

      researchmap

    ▼display all

    Misc.

    • On the regulatory roole of the epsilon subunit in ATP synthase Invited

      Yasuyuki KATO-YAMADA

      Seikagaku81 ( 11 )   11 2009

      ▶ More details

      Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)   Publisher：Japanese Biochemical Society  

      researchmap

    • 3P326 Fluorescent visualization of intracellular ATP(Bioimaging,Poster Presentations)

      Imamura Hiromi, Kim Huynh Nhat Phuong, Saito Kenta, Iino Ryota, Kato-Yamada Yasuyuki, Nagai Takeharu, Noji Hiroyuki

      Biophysics47 ( 1 ) S284   20 11 2007

      ▶ More details

      Language：English   Publisher：The Biophysical Society of Japan  

      DOI： 10.2142/biophys.47.S284_3

      CiNii Article

      researchmap

    Professional Memberships

    •  
      American Society for Biochemistry and Molecular Biology

      ▶ More details

    •  
      日本生物物理学会

      ▶ More details

    •  
      日本生化学会

      ▶ More details

    Research Projects

    • ATP合成酵素のATPモーターとプロトンモーターをつなぐ分子内クラッチ

      日本学術振興会  科学研究費助成事業 

      山田 康之

      ▶ More details

      4 2015 - Present

      Authorship：Principal investigator  Grant type：Competitive

      ATP合成酵素に見られる、条件的脱共役状態の分子機構を明らかにする。

      researchmap

    • Structural and physiological analyses of the pressure adaptation in the deep-sea enzyme.

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

      KATO Chiaki, WATANABE Nobuhisa, YAMADA Yasuyuki

      ▶ More details

      4 2013 - 3 2017

      Grant number：25450121

      Grant amount：\4940000 （ Direct Cost: \3800000 、 Indirect Cost：\1140000 ）

      3-Isopropylmalate dehydrogenase (IPMDH) from the extreme piezophile Shewanella benthica (SbIPMDH) is more pressure-tolerant than that from the atmospheric pressure-adapted Shewanella oneidensis (SoIPMDH). To understand the molecular mechanisms of this pressure tolerance, we analyzed mutated enzymes. The results indicate that only a single mutation at position 266, corresponding to Ala (SbIPMDH) and Ser (SoIPMDH), essentially affects activity under higher-pressure (HP) conditions. 3D-structural analyses of SoIPMDH suggests that penetration of three water molecules into the cleft around Ser266 under HP conditions could reduce the activity of the wild-type enzyme; however, no water molecule is observed in the Ala266 mutant. Water penetration into the cleft under HP conditions would appear to be less frequent than for the atmospheric-adapted SoIPMDH due to the reduced probability of forming a hydrogen bond, and as a consequence, SbIPMDH could adapt to the HP conditions of the deep sea.

      researchmap

    • 枯草菌ATP合成酵素の活性調節の包括的理解

      日本学術振興会  科学研究費助成事業 

      ▶ More details

      4 2011 - 3 2016

      Grant type：Competitive

      枯草菌ATP合成酵素の活性調節機構の解明

      researchmap

    • ATP合成酵素の回転モータ制御の分子機構

      文部科学省  科学研究費助成事業 

      ▶ More details

      4 2006 - 3 2011

      Grant type：Competitive

      代表：久堀徹

      researchmap

    • ATP合成酵素のεサブユニットへのATP結合と活性調節

      日本学術振興会  科学研究費助成事業 

      山田 康之

      ▶ More details

      4 2006 - 3 2008

      Grant number：18770118

      Grant type：Competitive

      これまでの研究結果から、ATR合成酵素複合体中でもεサブユニットがATP結合能を持つ事が強く示唆された。
      そこで、本年度発表の論文では、様々なATP結合能を持つアラニン置換変異体εサブユニットを含む、ATP合成酵素のα_3β_3γε部分複合体のATPase活性調節を詳細に検討した。その結果、阻害に直接関与すると考えられる残基をアラニンに置換した変異体を唯一の例外とし、それ以外の変異体では、εサブユニットへのATP結合が弱ければ弱いほど、ATPase活性を阻害する効果が強くなる事が明らかになった。また、εサブユニットへのATP結合が活性調節の際に起こるεサブユニットの構造変化のきっかけであるかを調べた。このために、α、βサブユニットのATP結合能を無くした変異体α3_β_3γεを作成し、ATPの添加に伴うεサブユニットの構造変化を検討した。その結果、変異体ではATPの添加に伴うεサブユニットの構造変化は起こらない事が明らかになった。このことは、εサブユニットへのATP結合のみではεサブユニットの構造変化は起こらず、触媒サブユニットであるβサブユニットへのATP結合によって構造変化が引き起こされる事を意味する。εサブユニットへのATP結合には、一旦活性化した複合体を活性化状態に保つ働きがあると考えられる。実際、野生型のα_3β_3γε複合体では、一旦活性化した複合体は、ATP濃度を下げても活性化状態を保つが、ATP結合の弱まった変異体εサブユニットを含むα_3β_3γε複合体では、反応液のATP濃度を低下させる事で活性化した複合体の再不活性化が観察された。
      これらの結果より、ATP合成酵素の新たな活性調節機構を提案する事が出来た

      researchmap

    • ATP合成酵素のεサブユニットによる制御機構

      日本学術振興会  科学研究費助成事業 

      山田 康之

      ▶ More details

      2000 - 2002

      Grant number：00J09995

      Grant amount：\3900000 （ Direct Cost: \3900000 ）

      本年度は、ATP合成酵素のεサブユニットにATPが結合するという、全く新しい知見を得た。
      ATP合成酵素の部分複合体であり、α_3β_3γεというサブユニット組成を持つF_1-ATPaseには、3つずつあるαとβに1つずつ、合計6カ所のATP結合部位が存在することが知られている。このうちのβサブユニットにあるATP結合部位が、ATP合成、加水分解の触媒部位である。これまでに、F_1-ATPaseのその他のサブユニットにATPが結合するという報告はない。
      本年度私は、好熱菌由来のF_1-ATPase(TF_1)のεサブユニットにATPが結合することを見出した。εサブユニット単独で大量発現させ調製した標品を用いて実験を行った。εサブユニットとATPの結合は強く、両者の複合体をゲル濾過HPLCで単離することができた。加えるATPの量を変化させ、結合の量比を見積もったところ、1:1の結合であった。ATPの代わりにADPを用いると結合は見られなかった。また結合の特異性は高く、GTPなどATP以外のヌクレオチド三リン酸は結合しなかった。
      ATP合成酵素複合体やその部分複合体であるF_1-ATPaseに含まれるεサブユニットへのATPの結合はαサブユニットやβサブユニットへの結合と区別することが困難で、現在までには確認できていない。
      もしεサブユニットへのATPの結合が、ATP合成酵素複合体中でも起こるものであれば、εサブユニットによる活性制御と直接関与する重要なものと考えられる。

      researchmap

    • εサブユニットによるATP合成酵素の調節機構

      日本学術振興会  科学研究費助成事業 

      山田 康之

      ▶ More details

      1998 - 1999

      Grant number：98J00185

      Grant amount：\1800000 （ Direct Cost: \1800000 ）

      researchmap

    ▼display all

    Industrial property rights

    • Fluorescently labeled fusion protein for assaying adenosine triphosphate.

      Hiroyuki Noji, Hiromi Imamura, Ryota Iino, Yasuyuki Yamada

      ▶ More details

      Patent/Registration no：US Patent 08524447  Date issued：3 9 2013

      researchmap