1.
Yoneyama, M. et al. Shared and Unique Functions of the DExD/H-Box
Helicases RIG-I, MDA5, and LGP2 in Antiviral Innate Immunity. The Journal
of Immunology 175, 2851–2858 (2005).
2.
Kato, H. et al. Cell type-specific involvement of RIG-I in antiviral response.
Immunity 23, 19–28 (2005).
3.
Kato, H. et al. Differential roles of MDA5 and RIG-I helicases in the
recognition of RNA viruses. Nature 441, 101–105 (2006).
4.
Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in
double-stranded RNA-induced innate antiviral responses. Nature Immunology 5,
730–737 (2004).
5.
Andrejeva, J. et al. The V proteins of paramyxoviruses bind the IFN-inducible
RNA helicase, mda-5, and inhibit its activation of the IFN-β promoter.
Proceedings of the National Academy of Sciences of the United States of
America 101, 17264–17269 (2004).
6.
Rothenfusser, S. et al. The RNA Helicase Lgp2 Inhibits TLR-Independent
Sensing of Viral Replication by Retinoic Acid-Inducible Gene-I. The Journal of
Immunology 175, 5260–5268 (2005).
7.
Saito, T. et al. Regulation of innate antiviral defenses through a shared repressor
domain in RIG-1 and LGP2. Proceedings of the National Academy of Sciences
of the United States of America 104, 582–587 (2007).
8.
Kawai, T. et al. IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I
interferon induction. Nature Immunology 6, 981–988 (2005).
- 62 -
9.
Seth, R. B., Sun, L., Ea, C. K. & Chen, Z. J. Identification and characterization
of MAVS, a mitochondrial antiviral signaling protein that activates NF-κB and
IRF3. Cell 122, 669–682 (2005).
10.
Takahasi, K. et al. Solution structures of cytosolic RNA sensor MDA5 and
LGP2 C-terminal domains: Identification of the RNA recognition loop in RIGI-like receptors. Journal of Biological Chemistry 284, 17465–17474 (2009).
11.
Satoh, T. et al. LGP2 is a positive regulator of RIG-I- and MDA5-mediated
antiviral responses. Proceedings of the National Academy of Sciences of the
United States of America 107, 1512–1517 (2010).
12.
Yoneyama, M., Onomoto, K., Jogi, M., Akaboshi, T. & Fujita, T. Viral RNA
detection by RIG-I-like receptors. Current Opinion in Immunology 32, 48–53
(2015).
13.
Rehwinkel, J. & Gack, M. U. RIG-I-like receptors: their regulation and roles in
RNA sensing. Nature Reviews Immunology 20, 537–551 (2020).
14.
Takahasi, K. et al. Nonself RNA-Sensing Mechanism of RIG-I Helicase and
Activation of Antiviral Immune Responses. Molecular Cell 29, 428–440 (2008).
15.
Ramanathan, A. et al. The autoinhibitory CARD2-Hel2i Interface of RIG-I
governs RNA selection. Nucleic Acids Research 44, 896–909 (2016).
16.
Peisley, A., Wu, B., Yao, H., Walz, T. & Hur, S. RIG-I Forms SignalingCompetent Filaments in an ATP-Dependent, Ubiquitin-Independent Manner.
Molecular Cell 51, 573–583 (2013).
17.
Devarkar, S. C., Schweibenz, B., Wang, C., Marcotrigiano, J. & Patel, S. S.
RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for
- 63 -
Kinetic Proofreading of RNAs and Oligomerization. Molecular Cell 72, 355368.e4 (2018).
18.
Myong, S. et al. Cytosolic viral sensor RIG-I is a 5’-triphosphate-dependent
translocase on double-stranded RNA. Science 323, 1070–1074 (2009).
19.
Kumar, H. et al. Essential role of IPS-1 in innate immune responses against
RNA viruses. Journal of Experimental Medicine 203, 1795–1803 (2006).
20.
Loo, Y.-M. et al. Distinct RIG-I and MDA5 Signaling by RNA Viruses in
Innate Immunity. Journal of Virology 82, 335–345 (2008).
21.
Hornung, V. et al. 5′-Triphosphate RNA is the ligand for RIG-I. Science 314,
994–997 (2006).
22.
Pichlmair, A. et al. RIG-I-mediated antiviral responses to single-stranded RNA
bearing 5′-phosphates. Science 314, 997–1001 (2006).
23.
Schmidt, A. et al. 5′-triphosphate RNA requires base-paired structures to
activate antiviral signaling via RIG-I. Proceedings of the National Academy of
Sciences of the United States of America 106, 12067–12072 (2009).
24.
Schlee, M. et al. Recognition of 5′ Triphosphate by RIG-I Helicase Requires
Short Blunt Double-Stranded RNA as Contained in Panhandle of NegativeStrand Virus. Immunity 31, 25–34 (2009).
25.
Kato, H. et al. Length-dependent recognition of double-stranded ribonucleic
acids by retinoic acid-inducible gene-I and melanoma differentiation-associated
gene 5. Journal of Experimental Medicine vol. 205 1601–1610 at
https://doi.org/10.1084/jem.20080091 (2008).
- 64 -
26.
Marques, J. T. et al. A structural basis for discriminating between self and
nonself double-stranded RNAs in mammalian cells. Nature Biotechnology 24,
559–565 (2006).
27.
Duic, I. et al. Viral RNA recognition by LGP2 and MDA5, and activation of
signaling through step-by-step conformational changes. Nucleic Acids Research
48, 11664–11674 (2020).
28.
Funabiki, M. et al. Autoimmune Disorders Associated with Gain of Function of
the Intracellular Sensor MDA5. Immunity 40, 199–212 (2014).
29.
Berke, I. C. & Modis, Y. MDA5 cooperatively forms dimers and ATP-sensitive
filaments upon binding double-stranded RNA. EMBO Journal 31, 1714–1726
(2012).
30.
Saito, T. & Gale, M. Differential recognition of double-stranded RNA by RIGI-like receptors in antiviral immunity. Journal of Experimental Medicine 205,
1523–1527 (2008).
31.
Onomoto, K., Onoguchi, K., Takahasi, K. & Fujita, T. Type I interferon
production induced by RIG-I-like receptors. Journal of Interferon and Cytokine
Research 30, 875–881 (2010).
32.
Onoguchi, K., Yoneyama, M. & Fujita, T. Retinoic acid-inducible Gene-I-Like
receptors. Journal of Interferon and Cytokine Research 31, 27–31 (2011).
33.
Takahasi, K. et al. Identification of a new autoinhibitory domain of interferonbeta promoter stimulator-1 (IPS-1) for the tight regulation of oligomerizationdriven signal activation. Biochemical and Biophysical Research
Communications 517, 662–669 (2019).
- 65 -
34.
Abe, H. et al. Priming Phosphorylation of TANK-Binding Kinase 1 by IkappaB
Kinase beta Is Essential in Toll-Like Receptor 3/4 Signaling. Mol Cell Biol 40,
1–14 (2020).
35.
Fujita, T., Shibuyà, H., Hotta, H., Yamanishi, K. & Taniguchi, T. Interferon-β
gene regulation: Tandemly repeated sequences of a synthetic 6 bp oligomer
function as a virus-inducible enhancer. Cell 49, 357–367 (1987).
36.
Takamatsu, S. et al. Functional Characterization of Domains of IPS-1 Using an
Inducible Oligomerization System. PLoS ONE 8, (2013).
37.
Yoneyama, M. et al. Direct triggering of the type I interferon system by virus
infection : activation of a transcription factor complex containing IRF-3 and
CBP / p300. 17, 1087–1095 (1998).
38.
Mori, M. et al. Identification of Ser-386 of Interferon Regulatory Factor 3 as
Critical Target for Inducible Phosphorylation That Determines Activation.
Journal of Biological Chemistry 279, 9698–9702 (2004).
39.
Kato, H., Takahasi, K. & Fujita, T. RIG-I-like receptors: Cytoplasmic sensors
for non-self RNA. Immunological Reviews 243, 91–98 (2011).
40.
Ouda, R. et al. Retinoic acid-inducible gene I-inducible miR-23b inhibits
infections by minor group rhinoviruses through down-regulation of the very low
density lipoprotein receptor. Journal of Biological Chemistry 286, 26210–26219
(2011).
41.
Kageyama, M. et al. 55 Amino acid linker between helicase and carboxyl
terminal domains of RIG-I functions as a critical repression domain and
- 66 -
determines inter-domain conformation. Biochemical and Biophysical Research
Communications 415, 75–81 (2011).
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Chapter 6
Acknowledgements
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Acknowledgements
Thanks to all Fujita lab members, I could complete my research.
Specially thanks to Professor Fujita. He introduced RIG-I protein and guided me to
innate immune field. Thanks to his massive knowledges and experiment technique, I
was able to try lots of interesting experiments. Especially, his attitude towards
research always inspires me not to lose my own way.
Also, thanks to Professor Shige H. Yoshimura, allowed me to use AFM machine.
I appreciate to Ivana for helping me to plan RIG-I experiments and teaching
experiments including AFM, protein purification, Seong-Wook Oh for advice and
support, and Koshiba-san, who is working for lab as secretary, for many helps.
I appreciate to Prof. Noda and three referees for great helps for reviewing my thesis. I
could study how to present scientific results correctly and how to make precise
statistical analysis.
Lastly, I sincerely appreciate my family for always giving me unstinting support and
love.
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This study was supported by research grants from Japan Agency for Medical Research
and Development: Research Program on Emerging and Re-emerging Infectious
Diseases [jp19fk0108081h1001, jp20fk0108081h1202 to F.T.]; Japan Society for the
Promotion of Science; Fund for the Promotion of Joint International Research:
Fostering Joint International Research (B) [18KK0232 to F.T.]; Core to Core Program:
Grant-in-Aid for Scientific Research ‘B’ [18H02344 to F.T.]. It was also funded by
the Deutsche Forschungsgemeinschaft (German Research Foundation) under
Germany’s Excellence Strategy–EXC2151–390873048 and TRR237, and Deutsche
Forschungsgemeinschaft
(DFG,
German
Research
Foundation)
EXC
2151:
ImmunoSensation2, Project number 390873048; DFG TRR 237, Project number
369799452 (B22). Funding for open access charge: DFG ImmunoSensation2.
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This thesis is based on the material contained in the following scholarly paper:
Mechanisms of length‐dependent recognition of viral double‐stranded RNA by
RIG‐I
Jung Hyun Im, Ivana Duic, Shige H. Yoshimura, Koji Onomoto, Mitsutoshi
Yoneyama, Hiroki Kato and Takashi Fujita
Scientific Reports, Nature Portfolio, volume 13, article number 6318
Published: 18 April 2023
DOI: 10.1038/s41598-023-33208-w
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...