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Key Research Publications from Graduate School of Frontier Biosciences

Nature Cell Biology doi:10.1038/ncb1821 (published online Jan 11, 2009)

Involvement of linear polyubiquitylation of NEMO in NF-κB activation

Nuclear factor-κB (NF-κB) is a key transcription factor in inflammatory, anti-apoptotic and immune processes. The ubiquitin pathwayis crucial in regulating the NF-κB pathway. We have found that the LUBAC ligase complex, composed of the two RING finger proteins, HOIL-1L and HOIP, conjugates a head-to-tail-linked linear polyubiquitin chain to substrates. Here, we demonstrate that LUBAC activates the canonical NF κB pathway by binding to NEMO (NF-κB essential modulator, also called IKKγ) and conjugates linear polyubiquitin chains onto specific Lys residues in the CC2LZ domain of NEMO in a Ubc13-independent manner. Moreover, in HOIL-1 knockout mice and cells derived from these mice, NF-κB signalling induced by pro-inflammatory cytokines such as TNF α and IL 1β was suppressed, resulting in enhanced TNF αinduced apoptosis in hepatocytes of HOIL 1 knockout mice. These results indicate that LUBAC is involved in the physiological regulation of the canonical NF κB activation pathway through linear polyubiquitylation of NEMO.

19136968 Biomolecular Networks Laboratories, Cell Biology and Metabolism Group (Prof. Iwai)
Nature . Vol 451 | 24 January 2008

Translocation of many soluble proteins across cell membranes occurs in an ATPase-driven manner. For construction of the bacterial flagellum responsible for motility, most of the components are exported by the flagellar protein export apparatus. The FliI ATPase is required for this export, and its ATPase activity is regulated by FliH; however, it is unclear how the chemical energy derived from ATP hydrolysis is used for the export process. Here we report that flagellar proteins of Salmonella enterica sarvor Typhimuriumare exported even in the absence of FliI. A fliH fliIdouble null mutant was weakly motile. Certain mutations in FlhA or FlhB, which form the core of the export gate, substantially improved protein export and motility of the double null mutant. Furthermore, proton motive force was essential for the export process. These results suggest that the FliH FliI complex facilitates only the initial entry of export substrates into the gate, with the energy of ATP hydrolysis being used to disassemble and release the FliH FliI complex from the protein about to be exported. The rest of the successive unfolding/translocation process of the substrates is driven by proton motive force.

18216858 Protonic NanoMachine Laboratory
(Prof. Namba)

Nature .
450, 285-288 (2007)

17994097 Developmental Genetics Laboratory
(Prof. Hamada)

Nature Structrural & Molecular Biology. 14(10):968-973 (2007)

Myosin-V is a molecular motor that walks along an actin filamment for carrying cargo. Single molecule analysis has revealed that myosin-V makes two 90 degrees rotations per 36nm-step.The direction of rotation was random, indicating that the rotation is driven by thermal fluctuation. We concluded that myosin-V is likely moved by a biased Brownian rotation.

17891151 Soft Biosystem Laboratory
(Prof. Yanagida)
    Molecular Cell, 26 (2): 231-243 (27 April 2007).

Human Cell Biology Laboratory(Prof. Tanaka)
    Nature Cell Biology, (Published online: December 3, 2006).

Laboratory of Stem Cell Pathology(Prof. Nakano)
    Nature Cell Biology, (Published online: December 10, 2006).

Biomolecular Dynamics Laboratory
(Prof. Yoneda)
    Nature, 443:998-1002 (2006) (26 Oct. 2006)
Chronic polyarthritis caused by mammalian DNA that escapes from degradation in macrophages.

Laboratory of Genetics (Prof. Nagata)
    Nature Immunology, 7: 971 - 977 (2006) (Published online: 6 August 2006; | doi:10.1038/ni1373)
Toll-like receptor mediated regulation of zinc homeostasis influences dendritic cell function.

Laboratory of Developmental Immunology (Prof. Hirano)
    Neuron, 50, 841-853 (2006), (June 15th, 2006)
PFGF as a Target-Derived Chemoattractant for Developing Motor Axons Genetically Programmed by the LIM Code.

Cellular and Molecular Neurobiology Group
    Physical Review Letters, 96, 194101 (May 2006)
Determination of a Coupling Function in Multicoupled Oscillators.

Nonequilibrium Physics Group (Prof. Kinoshita)

Taniguchi, Y., Nishiyama, M., Ishii, Y. and Yanagida, T.Entropy rectifies the Brownian steps of kinesin.

Nature Chemical Biology 1, 346-351 (2005)

Heat or thermal noise causes a serious problem to make some artificial machines smaller to nanometer level. We found a mechanism where a nanometer-sized motor protein, kinesin, uses the thermal noise to move, contrary to well-known machines. It is expected that the application of proteins to nano-technology may enable us to create new nano-machines that function even if surrounded by the thermal noise.


Yoshida H, Kawane K, Koike M, Mori Y, Uchiyama Y, Nagata S.Phosphatidylserine-dependent engulfment by macrophages of nuclei from erythroid precursor cells.

Nature, 437:754-8(Sep29 2005)

June 2005
Tachibanaki, S, Arinobu, D, Shimauchi-Matsukawa, Y, Tsushima, S. and Kawamura, S.Highly effective phosphorylation by G protein-coupled receptor kinase 7 of light-activated visual pigment in cones.
PNAS, 102: 9329-9334 (28 June 2005)

June 2005
Martomo SA, Yang WW, Wersto RP, Ohkumo T, Kondo Y, Yokoi M, Masutani C, Hanaoka F, Gearhart PJ.Different mutation signatures in DNA polymerase {eta}- and MSH6-deficient mice suggest separate roles in antibody diversification.
PNAS, 102(24):8656-8661(6 Jun 2005)

May 2005
Sugasawa K, Okuda Y, Saijo M, Nishi R, Matsuda N, Chu G, Mori T, Iwai S, Tanaka K, Tanaka K, Hanaoka F. UV-Induced Ubiquitylation of XPC Protein Mediated by UV-DDB-Ubiquitin Ligase Complex
Cell, 121(3): 387-400 (6 May 2005)

The xeroderma pigmentosum group C (XPC) protein complex plays a key role in recognizing DNA damage throughout the genome for mammalian nucleotide excision repair (NER). Ultraviolet light (UV)-damaged DNA binding protein (UV-DDB) is another complex that appears to be involved in the recognition of NER-inducing damage, although the precise role it plays and its relationship to XPC remain to be elucidated. Here we show that XPC undergoes reversible ubiquitylation upon UV irradiation of cells and that this depends on the presence of functional UV-DDB activity. XPC and UV-DDB were demonstrated to interact physically, and both are polyubiquitylated by the recombinant UV-DDB-ubiquitin ligase complex. The polyubiquitylation altered the DNA binding properties of XPC and UV-DDB and appeared to be required for cell-free NER of UV-induced (6-4) photoproducts specifically when UV-DDB was bound to the lesion. Our results strongly suggest that ubiquitylation plays a critical role in the transfer of the UV-induced lesion from UV-DDB to XPC.
Feb 2005
Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T, Koide T, Kitsukawa T, Hamada S, and Yagi T. Monoallelic yet combinatorial expression of variable exons of the CNR/Protocadherin-a gene cluster in single neurons.
Nature Genetics,37(2):171-176 (9 Feb 2005)

Diverse protocadherin-a genes (Pcdha, also called cadherinrelated neuronalreceptor or CNR) are expressed in the vertebrate brain. Their genomicorganization involves multiple variable exons and a set of constant exons,similar to the immunoglobulin (Ig) and T-cell receptor (TCR) genes. This iversity can be used to distinguish neurons. Using polymorphisms that distinguish the C57BL/6 and MSM mouse strains, we analyzed the allelic expression of the Pcdha gene cluster in individual neurons. Single-cell analysis of Purkinje cells using multiple RT-PCR reactions showed the monoallelic and combinatorial expression of each variable exon in the Pcdha genes. This report is the first description to our knowledge of the allelic expression of a diversified receptor family in the central nervous system. The allelic and combinatorial expression of distinct variable exons of the Pcdha genes is a potential mechanism for specifying neuron identity in the brain.
  Jan 2005
Yoshida H, Okabe Y, Kawane K, Fukuyama H, Nagata S. Lethal anemia caused by interferon-β produced in mouse embryos carrying undigested DNA.
Nature Immunology,6(1):49-56(Jan 2005).

The livers of DNase II-deficient mouse embryos contain many macrophages carrying undigested DNA, and the embryos die in utero. Here we report that erythroid precursor cells underwent apoptosis in the livers of DNase II-deficient embryos and that in the liver, interferon-beta mRNA was expressed by the resident macrophages. When the DNase II-deficient mice were crossed with mice deficient in type I interferon receptor, the resultant 'double-mutant' mice were born healthy. The double-mutant embryos expressed interferon-beta mRNA, but the expression of a subset of the interferon-responsive genes dysregulated in DNase II-deficient embryos was restored to normal. These results indicate that the inability to degrade DNA derived from erythroid precursors results in interferon-beta production that induces expression of a specific set of interferon-responsive genes associated with embryonic lethality in DNase II-deficient mice.

  Jan 2005
Shaikh TR, Thomas DR, Chen JZ, Samatey FA, Matsunami H, Imada K, Namba K, Derosier DJ. A partial atomic structure for the flagellar hook of Salmonella typhimurium.
PNAS, 102(4): 1023-8(25 Jan 2005)

Oct 2004
Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Kitao A, Namba K.Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.
, 431(7012): 1062-8 (28 Oct 2004)

*Comment in: Molecular motors: smooth coupling in Salmonella by Surridge C.
Horibata K, Iwamoto Y, Kuraoka I, Jaspers NG, Kurimasa A, Oshimura M, Ichihashi M, Tanaka K. Complete absence of Cockayne syndrome group B gene product gives rise to UV-sensitive syndrome but not Cockayne syndrome.
PNAS, 101(43):15410-5(26 Oct 2004)

*Comment in: The many faces of Cockayne syndrome by Spivak G.

Watanabe TM, Tanaka H, Iwane AH, Maki-Yonekura S, Homma K, Inoue A, Ikebe R, Yanagida T, Ikebe M. A one-headed class V myosin molecule develops multiple large (approximately 32-nm) steps successively.
PNAS, 101(26): 9630-5 (29 June 2004)
  May 2004 Hanayama, R., Tanaka, M., Miyasaka, K., Aozasa, K., Koike, M.,
Uchiyama, Y., and Nagata, S. Autoimmune disease and impaired uptake of
apoptotic cells in MFG-E8-deficient mice.
Science, 304:1147-1150 (2004)

Yamashita, S.*, Miyagi, C.*, Fukada, T., Kagara, N., Che, Y.S. and Hirano, T. (* equally contributed) Zinc transporter LIVI controls epithelial-mesenchymal transition in zebrafish gastrula organizer.
Nature, doi:10.1038/nature02545. Published online 5 May 2004

Yamamoto M, Saijoh Y, Perea-Gomez A, Shawlot W, Behringer RR, Ang SL, Hamada H, Meno C. Nodal antagonists regulate formation of the anteroposterior axis of the mouse embryo.
Nature, 428: 387-392 (2004).

Lee, S. J., Sekimoto, T., Yamashita, E., Nagoshi, E., Nakagawa, A., Imamoto, N., Yoshimura, M., Sakai, H., Chong, K. T., Tsukihara, T. and Yoneda, Y. The structure of importin b bound to SREBP-2: Insights into nuclear import of a transcription factor.
Science, 302: 1571-1575 (2003)


Nishimoto S, Kawane K, Watanabe-Fukunaga R, Fukuyama H, Ohsawa Y, Uchiyama Y, Hashida N, Ohguro N, Tano Y, Morimoto T, Fukuda Y, Nagata S. Nuclear cataract caused by a lack of DNA degradation in the mouse eye lens.
Nature, 424: 1071-1074 (2003)


Yonekura K, Maki-Yonekura S, Namba K. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
Nature, 424: 643-650 (2003)


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