Naofumi Handa - My portal

Profile Information

Affiliation: Department of Microbiology, University of California, Davis

Degree: 博士（医学）(東京大学)

J-GLOBAL ID: 200901085565992027
researchmap Member ID: 5000090787

External link: http://www.researchgate.net/profile/Naofumi_Handa/#target-disciplines

Research Interests

Research Areas

Research History

Apr, 2011

University of California, Davis
Oct, 2004 - Mar, 2011

Assistant Professor, University of Tokyo

Papers

Sae2 promotes DNA damage resistance by removing the Mre11-Rad50-Xrs2 complex from DNA and attenuating Rad53 signaling

Huan Chen, Roberto A. Donnianni, Naofumi Handa, Sarah K. Deng, Julyun Oh, Leonid A. Timashev, Stephen C. Kowalczykowski, Lorraine S. Symington

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(15) E1880-E1887, Apr, 2015 Peer-reviewed
MCM8-9 complex promotes resection of double-strand break ends by Mre11-Rad50-Nbs1 complex

HANDA Naofumi

Nature Communications, 6(7744), 2015 Peer-reviewed
The Third Exon of the Budding Yeast Meiotic Recombination Gene HOP2 Is Required for Calcium-dependent and Recombinase Dmc1-specific Stimulation of Homologous Strand Assimilation

Yuen-Ling Chan, M. Scott Brown, Daoming Qin, Naofumi Handa, Douglas K. Bishop

JOURNAL OF BIOLOGICAL CHEMISTRY, 289(26) 18076-18086, Jun, 2014 Peer-reviewed
Alteration of chi recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control

Liang Yang, Naofumi Handa, Bian Liu, Mark S. Dillingham, Dale B. Wigley, Stephen C. Kowalczykowski

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(23) 8907-8912, Jun, 2012 Peer-reviewed
Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, chi, by RecBCD enzyme

Naofumi Handa, Liang Yang, Mark S. Dillingham, Ichizo Kobayashi, Dale B. Wigley, Stephen C. Kowalczykowski

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(23) 8901-8906, Jun, 2012 Peer-reviewed
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species

Koji Yahara, Mikihiko Kawai, Yoshikazu Furuta, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori …

GENOME BIOLOGY AND EVOLUTION, 4(5) 628-640, 2012 Peer-reviewed
Cleavage of a model DNA replication fork by a methyl-specific endonuclease

Ken Ishikawa, Naofumi Handa, Lauren Sears, Elisabeth A. Raleigh, Ichizo Kobayashi

NUCLEIC ACIDS RESEARCH, 39(13) 5489-5498, Jul, 2011 Peer-reviewed
Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

Mikihiko Kawai, Yoshikazu Furuta, Koji Yahara, Takeshi Tsuru, Kenshiro Oshima, Naofumi Handa, Noriko Takahashi, Masaru Yoshida, Takeshi Azuma, Masahira Hattori …

BMC MICROBIOLOGY, 11 104, May, 2011 Peer-reviewed
Birth and death of genes linked to chromosomal inversion

Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori …

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(4) 1501-1506, Jan, 2011 Peer-reviewed
日本分離ピロリ菌４株の全ゲノム解読と種内比較解析についてのプログレス・レポート

小林一三, 河合幹彦, 矢原耕史, 古田芳一, 鶴剛史, 高橋規子, 半田直史, 吉田優, 大島健志朗, 内山郁夫 …

日本ヘリコバクター学会誌, 11(2), 2010
Single Molecule Analysis of a Red Fluorescent RecA Protein Reveals a Defect in Nucleoprotein Filament Nucleation That Relates to Its Reduced Biological Functions

Naofumi Handa, Ichiro Amitani, Nathan Gumlaw, Steven J. Sandler, Stephen C. Kowalczykowski

JOURNAL OF BIOLOGICAL CHEMISTRY, 284(28) 18664-18673, Jul, 2009 Peer-reviewed
Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex

Naofumi Handa, Asao Ichige, Ichizo Kobayashi

MICROBIOLOGY-SGM, 155(7) 2320-2332, Jul, 2009 Peer-reviewed
Cleavage of a model DNA replication fork by a Type I restriction endonuclease

Ken Ishikawa, Naofumi Handa, Ichizo Kobayashi

NUCLEIC ACIDS RESEARCH, 37(11) 3531-3544, Jun, 2009 Peer-reviewed
Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli

Naofumi Handa, Katsumi Morimatsu, Susan T. Lovett, Stephen C. Kowalczykowski

GENES & DEVELOPMENT, 23(10) 1234-1245, May, 2009 Peer-reviewed
ゲノムDNA二重鎖切断とその修復の高感度検出法の開発

小林一三, 半田直史, 河合幹彦, 高橋規子, 福田江里

Space Utilization Research, 25 39-41, 2009
Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity

Satona Ohno, Naofumi Handa, Miki Watanabe-Matsui, Noriko Takahashi, Ichizo Kobayashi

JOURNAL OF BACTERIOLOGY, 190(6) 2039-2049, Mar, 2008 Peer-reviewed
A RecA mutant, RecA(730), suppresses the recombination deficiency of the RecBC(1004)D-chi* interaction in vitro and in vivo

Naofumi Handa, Stephen C. Kowalczykowski

JOURNAL OF MOLECULAR BIOLOGY, 365(5) 1314-1325, Feb, 2007 Peer-reviewed
Hyperthermophilic DNA methyltransferase M.Pabl from the archaeon Pyrococcus abyssi

Miki Watanabe, Harurni Yuzawa, Naofumi Handa, Ichizo Kobayashi

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(8) 5367-5375, Aug, 2006 Peer-reviewed
The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation

F Chedin, N Handa, MS Dillingham, SC Kowalczykowski

JOURNAL OF BIOLOGICAL CHEMISTRY, 281(27) 18610-18617, Jul, 2006 Peer-reviewed
Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function

N Handa, Kobayashi, I

JOURNAL OF BACTERIOLOGY, 187(21) 7362-7373, Nov, 2005 Peer-reviewed

Books and Other Publications

相同組換え初期反応に重要なリセクション

半田直史

日本生化学会, 2010
Double-strand Breaks and their Consequences in Bacteria.

Kobayashi I, Handa N

In Encyclopedia of Life Sciences, A21652, Nature Publishing Group, Macmillan Reference Limited, London, 2009
組換え酵素

小林一三, 半田直史 (Role: Joint author, 生化学辞典第4版（今堀和友、山川民夫監修大島泰郎、鈴木紘一、脊山洋右、新井洋由、石浦章一、大隈良典、岸本健雄、正木春彦、山本一夫編） p380)

東京化学同人, 2007
RecBCD酵素の精製法

半田直史

朝倉書店, 2006
ゲノムを維持する組換え酵素の一分子生化学

半田直史

共立出版, 2005
ゲノムにとっての自己と非自己

半田直史, 小林一三 (Role: Joint author, 臨床免疫 31: 222-227.)

科学評論社, 1999
「利己的な遺伝子」にプログラムされる死

半田直史, 小林一三 (Role: Joint author, 遺伝 52: 61-67.)

裳華房, 1998
死をプログラムする利己的遺伝子

半田直史, 小林一三 (Role: Joint author, 最新医学 52: 2057-2064.)

最新医学社, 1997
死をプログラムする細菌の遺伝子

半田直史, 小林一三 (Role: Joint author, バイオクリニカ 12: 352-355.)

北隆館, 1997
相同組換えの機序と遺伝子治療への応用

半田直史, 小林一三 (Role: Joint author, 治療学 31: 429-433.)

ライフサイエンス出版, 1997

Research Projects

天然変性部位がＤＮＡの分解と組換えの切り替えを行う酵素の反応機構

科学研究費補助金新学術領域研究(領域型）, 文部科学省, 2010 - 2011

半田直史
自己ＤＮＡ識別修復酵素の自己ＤＮＡシグナル配列認識の分子機構

科学研究費補助金若手研究（B）, 日本学術振興会, 2010 - 2011

半田直史
ゲノムの高レベル進化速度に寄与する相同組換えの分子機構

研究助成, 住友財団, 2009 - 2010

半田直史
無害な細菌が病原性遺伝子を獲得して病原細菌になることを防ぐ機構

研究助成, 武田科学振興財団, 2009 - 2010

半田直史
ゲノムに潜む全く新しい構造と機能をもつDNaseファミリーの探索と解析

研究助成, 加藤記念財団, 2008 - 2009

半田直史
微生物に病原性をもたらす「病原ゲノム・アイランド」の取り込みに関与するDNA識別/排除機構の研究

科学研究助成, 内藤記念財団, 2007 - 2008

半田直史
自己ゲノムDNAを識別して修復するATP駆動モーターの一分子生化学

科学研究費補助金特定領域研究, 文部科学省, 2007 - 2008

半田直史
病原性薬剤耐性等の遺伝子の導入に対して細菌が備えるバリアーと細菌の生死

科学研究費補助金若手研究（B）, 日本学術振興会, 2007 - 2008

半田直史
ゲノム分解・修復マシーンによる「自己」ゲノム識別の一分子可視化解析

研究助成, 光科学技術研究振興財団, 2005 - 2006

半田直史
ゲノム維持ナノマシン:DNA分解修復を支配するATP駆動モーターの一分子生化学

科学研究費補助金特定領域研究, 文部科学省, 2005 - 2006

半田直史
非自己ゲノムを分解し、自己ゲノムを修復する組換え酵素の「一分子」遺伝学

科学研究費補助金若手研究（B）, 日本学術振興会, 2005 - 2006

半田直史