Welcome to Yamaguchi lab (OCARINA 05)

The Osaka City University Advanced Research Institute for Natural Science and Technology

 
 

I have been working in the field of toxin-antitoxin (TA) systems in Escherichia coli. Each TA system is encoded by two small genes, which usually overlap by a few bases. A toxin and its cognate antitoxin form a stable TA complex, which blocks the function of the toxin.  Almost all bacteria contain a number of TA systems, targeting various cellular functions from DNA replication, mRNA stability, protein synthesis and cell wall biosynthesis to regulate cell growth and death. As the antitoxin is less stable than the toxin in the cell, it has to be constantly produced to inhibit the toxin. Under stress conditions, antitoxins are digested by stress-induced proteases to release free toxins, resulting in cell growth arrest and eventual cell death. A number of TA systems appear to be related to the pathogenicity of a bacterium. The TA systems in M. tuberculosis may play important roles in the maintenance of the extremely long dormancy of this pathogen inside macrophage.  On the basis of this idea, it is perhaps surprising that E. coli also contains comparatively a large number of TA systems. I am studying to understand the physiological functions of TA systems in bacteria.

 

Toxin-antitoxin systems

Yoshihiro Yamaguchi

Associate Professor


3-3-138 Sugimoto Sumiyoshi-ku,

Osaka, 558-8585, JAPAN

Email: yamaguchi( at )ocarina.osaka-cu.ac.jp

Phone: +81-6-6605-3709


Research interests: Programmed cell-death, Toxin-antitoxin systems

Education:

3/05   Ph.D. in Agriculture, Tohoku Univ., Sendai, Japan

3/02   M.S. in Agriculture, Tohoku Univ., Sendai, Japan

3/99   B.S. in Agriculture, Tokyo Univ. of Agriculture, Tokyo, Japan


Research Experience: 

2004 – 2006   Research Fellow of the Japan Society for the Promotion of Science (JSPS Research Fellow) at

                        Tohoku Univ., Sendai, Japan

2006 – 2010   Postdoctoral fellow at Robert Wood Johnson Medical School., Piscataway, USA

2010 – 2014   Research and teaching assistant III at Robert Wood Johnson Medical School., Piscataway,

                        USA

2014-present Associate professor at Osaka city university, Osaka, Japan

           

Awards:        Award for Excellence to Authors Publishing in Bioscience Biotechnology and Biochemistry

                        (2002)


                       Dean’s research awards for the best peer-reviewed publications of 2012 (2013)


Selected publications:

[1]Gene cloning and molecular characterization of lysine decarboxylase from Selenomonas

ruminantium delineate its evolutionary relationship to ornithine decarboxylases from eukaryotes.

J. Bacteriol., 182, 23, 6732-6741 (2000).

Yumiko Takatsuka, Yoshihiro Yamaguchi, Minenobu Ono, and Yoshiyuki Kamio


[2] Identification of a 22-kDa protein required for the degradation of Selenomonas

ruminantium lysine decarboxylase by ATP-dependent protease.

Biosci. Biotechnol. Biochem., 66, 6, 1431-1434 (2002).

Yoshihiro Yamaguchi, Yumiko Takatsuka, and Yoshiyuki Kamio

Award for Excellence to Authors Publishing in Bioscience Biotechnology and Biochemistry


[3] Characterization of a counterpart to mammalian ornithine decarboxylase antizyme in

prokaryotes.

J. Biol. Chem., 281, 7, 3995-4001 (2006).

Yoshihiro Yamaguchi, Yumiko Takatsuka, Senya Matsufuji, Yasuko Murakami, and Yoshiyuki Kamio


[4]  Polyamine-containing peptidoglycan and the regulation of biosynthesis of polyamines

by lysine/ornithine decarboxylase in Selnomonas ruminantium

Tanpakushitsu Kakusan Koso. 52, 3, 249-255 (2007).

Yoshiyuki Kamio, Yoshihiro Yamaguchi, and Yumiko Takatsuka


[5]Two segments in bacterial antizyme P22 are essential for binding and enhance

degradation of lysine/ornithine decarboxylase in Selenomonas ruminantium.

J. Bacteriol., 190, 1, 442-446 (2008)

Yoshihiro Yamaguchi, Yumiko Takatsuka, and Yoshiyuki Kamio


[6]Occurrence of agmatine pathway for putrescine synthesis in Selenomonas ruminatium.

Shaofu Liao, Phuntip Pooonpairoj, Kyong-Cheol Ko, Yumiko Takatsuka,

    Yoshihiro Yamaguchi, Naoki Abe, Jun Kaneko, and Yoshiyuki Kamio

Biosci. Biotechnol. Biochem. 72, 2, 445-455 (2008)


[7]    mRNA interferases, sequence-specific endoribonucleases from the toxin-antitoxin system.  (Review)

Yoshihiro Yamaguchi and Masayori Inouye

Prog. Mol. Biol. Transl. Sci. 85, 467-500 (2009)


[8]    Staphylococcus aureus YoeB homologues inhibit translation initiation

Satoshi Yoshizumi, Yonglong Zhang, Yoshihiro Yamaguchi, Ling Zhu,

Barry N. Kreiswirth and Masayori Inouye

J. Bacteriol., 191, 18, 5868-5872 (2009)


[9]  Characterization of YafO, an Escherichia coli toxin.

        Yonglong Zhang, Yoshihiro Yamaguchi and Masayori Inouye

        J. Biol. Chem., 284, 38, 25522-25531 (2009)


[10]  MqsR, a crucial regulator for quorum sensing and biofilm formation, is a

GCU-specific mRNA interferase in Escherichia coli.

Yoshihiro Yamaguchi and Masayori Inouye

J. Biol. Chem., 284, 42, 28746-28753 (2009)


[11]  Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase.

        Jung-Ho Park, Yoshihiro Yamaguchi and Masayori Inouye

FEBS lett., 585, 15, 2526-2532 (2011)


[12]  Regulation of growth and death in Escherichia coli by toxin-antitoxin systems.  (Review)

        Yoshihiro Yamaguchi and Masayori Inouye

Nat. Rev. Microbiol., 9, 11, 779-790 (2011)


[13]  Toxin-antitoxin systems in bacteria and archaea.   (Review)

        Yoshihiro Yamaguchi, Jung-Ho Park and Masayori Inouye

Annu. Rev. Genet., 45, 61-79 (2011)


[14]  Inhibition of specific gene expressions by protein-mediated mRNA interference.

        Yoshihiro Yamaguchi, Hirofumi Nariya, Jung-Ho Park and Masayori Inouye

Nat. Commun., 3, 3, 607 (2012)

“Dean’s research awards for the best peer-reviewed publications of 2012”


[15]  A novel membrane-bound toxin for cell division, CptA (YgfX), inhibits polymerization of cytoskeleton proteins, FtsZ and MreB, in Escherichia coli.

        Hisako Masuda, Qian Tan, Naoki Awano, Yoshihiro Yamaguchi and Masayori Inouye

FEMS. Microbiol. Lett., 328, 2, 174-181 (2012)


[16]  Identification of the first functional toxin-antitoxin system in Streptomyces.

        Laura Sevillano, Margarita Díaz, Yoshihiro Yamaguchi, Masayori Inouye and Ramón I.  Santamaría

PLoS. One., 9, 11, 779-790 (2012)


[17]  Intramolecular regulation of the sequence-specific mRNA interferase activity of MazF

     fused to a MazE fragment with a linker cleavable by specific proteases.

     Jung-Ho Park, Yoshihiro Yamaguchi and Masayori Inouye

     Appl. Environ. Microbiol., 78, 11, 3794-3799 (2012)


[18]  ACA-specific RNA sequence recognition is acquired via the loop 2 region of MazF  mRNA interferase.

     Jung-Ho Park, Satoshi Yoshizumi, Yoshihiro Yamaguchi, Kuen-Phon Wu and 

     Masayori Inouye

Proteins, 81, 5, 874-883 (2012)


[19]  Replacement of all arginine residues with canavanine in MazF-bs mRNA interferase changes its specificity.

     Yojiro Ishida, Jung-Ho Park, Lili Mao, Yoshihiro Yamaguchi, and  Masayori Inouye

    J. Biol. Chem., 288, 11, 7564-7571 (2013)


[20]  Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus

         subtilis

     Dhirendra K. Simanshu, Yoshihiro Yamaguchi, Jung-Ho Park, Masayori Inouye, and Dinshaw J. Patel

     Mol. Cell, Oct 8. (2013)


Book

Type II Toxin-Antitoxin Loci: The mazEF Family

Yoshihiro Yamaguchi and Masayori Inouye

Prokaryotic Toxin-Antitoxins, 107-136 (2013)