Biomolecules & Therapeutics

  • 제31권1호
  • /
  • Pages.48-58
  • /
  • 2023
  • /
  • 1976-9148(pISSN)
  • /
  • 2005-4483(eISSN)
한국응용약물학회 (The Korean Society of Applied Pharmacology)
권호 표지
DOI QR코드

DOI QR Code

Identification of Small GTPases That Phosphorylate IRF3 through TBK1 Activation Using an Active Mutant Library Screen

  • Jae-Hyun, Yu (Department of Pharmacology and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea) ;
  • Eun-Yi, Moon (Department of Bioscience and Biotechnology, Sejong University) ;
  • Jiyoon, Kim (Department of Pharmacology and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea) ;
  • Ja Hyun, Koo (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University)
  • 투고 : 2022.09.06
  • 심사 : 2022.09.26
  • 발행 : 2023.01.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Interferon regulatory factor 3 (IRF3) integrates both immunological and non-immunological inputs to control cell survival and death. Small GTPases are versatile functional switches that lie on the very upstream in signal transduction pathways, of which duration of activation is very transient. The large number of homologous proteins and the requirement for site-directed mutagenesis have hindered attempts to investigate the link between small GTPases and IRF3. Here, we constructed a constitutively active mutant expression library for small GTPase expression using Gibson assembly cloning. Small-scale screening identified multiple GTPases capable of promoting IRF3 phosphorylation. Intriguingly, 27 of 152 GTPases, including ARF1, RHEB, RHEBL1, and RAN, were found to increase IRF3 phosphorylation. Unbiased screening enabled us to investigate the sequence-activity relationship between the GTPases and IRF3. We found that the regulation of IRF3 by small GTPases was dependent on TBK1. Our work reveals the significant contribution of GTPases in IRF3 signaling and the potential role of IRF3 in GTPase function, providing a novel therapeutic approach against diseases with GTPase overexpression or active mutations, such as cancer.

키워드

과제정보

This work was supported by National Research Foundation of Korea grants funded by the Korea government (MSIP) (2021R1C1C1013323, 2021R1A4A5033289) as well as by the Creative-Pioneering Researchers Program and New Faculty Startup Fund from Seoul National University.

참고문헌

  1. Arbibe, L., Mira, J. P., Teusch, N., Kline, L., Guha, M., Mackman, N., Godowski, P. J., Ulevitch, R. J. and Knaus, U. G. (2000) Toll-like receptor 2-mediated NF-kappa B activation requires a Rac1-dependent pathway. Nat. Immunol. 1, 533-540. https://doi.org/10.1038/82797
  2. Balch, W. E. (1990) Small GTP-binding proteins in vesicular transport. Trends Biochem. Sci. 15, 473-477. https://doi.org/10.1016/0968-0004(90)90301-Q
  3. Beachboard, D. C., Park, M., Vijayan, M., Snider, D. L., Fernando, D. J., Williams, G. D., Stanley, S., McFadden, M. J. and Horner, S. M. (2019) The small GTPase RAB1B promotes antiviral innate immunity by interacting with TNF receptor-associated factor 3 (TRAF3). J. Biol. Chem. 294, 14231-14240. https://doi.org/10.1074/jbc.ra119.007917
  4. Bodur, C., Kazyken, D., Huang, K., Ekim Ustunel, B., Siroky, K. A., Tooley, A. S., Gonzalez, I. E., Foley, D. H., Acosta-Jaquez, H. A., Barnes, T. M., Steinl, G. K., Cho, K. W., Lumeng, C. N., Riddle, S. M., Myers, M. G., Jr. and Fingar, D. C. (2018) The IKK-related kinase TBK1 activates mTORC1 directly in response to growth factors and innate immune agonists. EMBO J. 37, 19-38. https://doi.org/10.15252/embj.201696164
  5. Boman, A. L., Taylor, T. C., Melancon, P. and Wilson, K. L. (1992) A role for ADP-ribosylation factor in nuclear vesicle dynamics. Nature 358, 512-514. https://doi.org/10.1038/358512a0
  6. Casalou, C., Ferreira, A. and Barral, D. C. (2020) The role of ARF family proteins and their regulators and effectors in cancer progression: a therapeutic perspective. Front. Cell Dev. Biol. 8, 217. https://doi.org/10.3389/fcell.2020.00217
  7. Chattopadhyay, S., Marques, J. T., Yamashita, M., Peters, K. L., Smith, K., Desai, A., Williams, B. R. and Sen, G. C. (2010) Viral apoptosis is induced by IRF-3-mediated activation of Bax. EMBO J. 29, 1762-1773. https://doi.org/10.1038/emboj.2010.50
  8. Chen, G. A., Lin, Y. R., Chung, H. T. and Hwang, L. H. (2017) H-Ras exerts opposing effects on type I interferon responses depending on its activation status. Front. Immunol. 8, 972. https://doi.org/10.3389/fimmu.2017.00972
  9. Cherfils, J. and Zeghouf, M. (2013) Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiol. Rev. 93, 269-309. https://doi.org/10.1152/physrev.00003.2012
  10. Ehrhardt, C., Kardinal, C., Wurzer, W. J., Wolff, T., von Eichel-Streiber, C., Pleschka, S., Planz, O. and Ludwig, S. (2004) Rac1 and PAK1 are upstream of IKK-epsilon and TBK-1 in the viral activation of interferon regulatory factor-3. FEBS Lett. 567, 230-238. https://doi.org/10.1016/j.febslet.2004.04.069
  11. Etienne-Manneville, S. and Hall, A. (2002) Rho GTPases in cell biology. Nature 420, 629-635. https://doi.org/10.1038/nature01148
  12. Fitzgerald, K. A., McWhirter, S. M., Faia, K. L., Rowe, D. C., Latz, E., Golenbock, D. T., Coyle, A. J., Liao, S. M. and Maniatis, T. (2003) IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat. Immunol. 4, 491-496. https://doi.org/10.1038/ni921
  13. Gao, P., Ascano, M., Wu, Y., Barchet, W., Gaffney, B. L., Zillinger, T., Serganov, A. A., Liu, Y., Jones, R. A., Hartmann, G., Tuschl, T. and Patel, D. J. (2013) Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell 153, 1094-1107. https://doi.org/10.1016/j.cell.2013.04.046
  14. Guiler, W., Koehler, A., Boykin, C. and Lu, Q. (2021) Pharmacological modulators of small GTPases of Rho family in neurodegenerative diseases. Front. Cell Neurosci. 15, 661612. https://doi.org/10.3389/fncel.2021.661612
  15. Gui, X., Yang, H., Li, T., Tan, X., Shi, P., Li, M., Du, F. and Chen, Z. J. (2019) Autophagy induction via STING trafficking is a primordial function of the cGAS pathway. Nature 567, 262-266. https://doi.org/10.1038/s41586-019-1006-9
  16. Hillis, D. M. and Bull, J. J. (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42, 182-192. https://doi.org/10.1093/sysbio/42.2.182
  17. Hiscott, J. (2007) Triggering the innate antiviral response through IRF-3 activation. J. Biol. Chem. 282, 15325-15329. https://doi.org/10.1074/jbc.R700002200
  18. Hodge, R. G. and Ridley, A. J. (2016) Regulating Rho GTPases and their regulators. Nat. Rev. Mol. Cell Biol. 17, 496-510. https://doi.org/10.1038/nrm.2016.67
  19. Husebye, H., Aune, M. H., Stenvik, J., Samstad, E., Skjeldal, F., Halaas, O., Nilsen, N. J., Stenmark, H., Latz, E., Lien, E., Mollnes, T. E., Bakke, O. and Espevik, T. (2010) The Rab11a GTPase controls Toll-like receptor 4-induced activation of interferon regulatory factor-3 on phagosomes. Immunity 33, 583-596. https://doi.org/10.1016/j.immuni.2010.09.010
  20. Ishikawa, H. and Barber, G. N. (2008) STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling. Nature 455, 674-678. https://doi.org/10.1038/nature07317
  21. Kahn, R. A., Volpicelli-Daley, L., Bowzard, B., Shrivastava-Ranjan, P., Li, Y., Zhou, C. and Cunningham, L. (2005) Arf family GTPases: roles in membrane traffic and microtubule dynamics. Biochem. Soc. Trans. 33, 1269-1272. https://doi.org/10.1042/BST0331269
  22. Kitai, Y., Takeuchi, O., Kawasaki, T., Ori, D., Sueyoshi, T., Murase, M., Akira, S. and Kawai, T. (2015) Negative regulation of melanoma differentiation-associated gene 5 (MDA5)-dependent antiviral innate immune responses by Arf-like protein 5B. J. Biol. Chem. 290, 1269-1280. https://doi.org/10.1074/jbc.M114.611053
  23. Liu, Y. P., Zeng, L., Tian, A., Bomkamp, A., Rivera, D., Gutman, D., Barber, G. N., Olson, J. K. and Smith, J. A. (2012) Endoplasmic  reticulum stress regulates the innate immunity critical transcription factor IRF3. J. Immunol. 189, 4630-4639. https://doi.org/10.4049/jimmunol.1102737
  24. Luo, F., Liu, H., Yang, S., Fang, Y., Zhao, Z., Hu, Y., Jin, Y., Li, P., Gao, T., Cao, C. and Liu, X. (2019) Nonreceptor tyrosine kinase c-Abland Arg-mediated IRF3 phosphorylation regulates innate immune responses by promoting type I IFN production. J. Immunol. 202, 2254-2265. https://doi.org/10.4049/jimmunol.1800461
  25. MacKeigan, J. P. and Krueger, D. A. (2015) Differentiating the mTOR inhibitors everolimus and sirolimus in the treatment of tuberous sclerosis complex. Neuro Oncol. 17, 1550-1559. https://doi.org/10.1093/neuonc/nov152
  26. Mao, Y., Luo, W., Zhang, L., Wu, W., Yuan, L., Xu, H., Song, J., Fujiwara, K., Abe, J. I., LeMaire, S. A., Wang, X. L. and Shen, Y. H. (2017) STING-IRF3 triggers endothelial inflammation in response to free fatty acid-induced mitochondrial damage in diet-induced obesity. Arterioscler. Thromb. Vasc. Biol. 37, 920-929. https://doi.org/10.1161/ATVBAHA.117.309017
  27. Ohman, T., Soderholm, S., Paidikondala, M., Lietzen, N., Matikainen, S. and Nyman, T. A. (2015) Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells. Proteomics 15, 2087-2097. https://doi.org/10.1002/pmic.201400586
  28. Patel, S. J., Liu, N., Piaker, S., Gulko, A., Andrade, M. L., Heyward, F. D., Sermersheim, T., Edinger, N., Srinivasan, H., Emont, M. P., Westcott, G. P., Luther, J., Chung, R. T., Yan, S., Kumari, M., Thomas, R., Deleye, Y., Tchernof, A., White, P. J., Baselli, G. A., Meroni, M., De Jesus, D. F., Ahmad, R., Kulkarni, R. N., Valenti, L., Tsai, L. and Rosen, E. D. (2022) Hepatic IRF3 fuels dysglycemia in obesity through direct regulation of Ppp2r1b. Sci. Transl. Med. 14, eabh3831. https://doi.org/10.1126/scitranslmed.abh3831
  29. Petrasek, J., Iracheta-Vellve, A., Csak, T., Satishchandran, A., Kodys, K., Kurt-Jones, E. A., Fitzgerald, K. A. and Szabo, G. (2013) STING-IRF3 pathway links endoplasmic reticulum stress with hepatocyte apoptosis in early alcoholic liver disease. Proc. Natl. Acad. Sci. U. S. A. 110, 16544-16549. https://doi.org/10.1073/pnas.1308331110
  30. Prakash, P. and Gorfe, A. A. (2013) Lessons from computer simulations of Ras proteins in solution and in membrane. Biochim. Biophys. Acta 1830, 5211-5218. https://doi.org/10.1016/j.bbagen.2013.07.024
  31. Punekar, S. R., Velcheti, V., Neel, B. G. and Wong, K. K. (2022) The current state of the art and future trends in RAS-targeted cancer therapies. Nat. Rev. Clin. Oncol. 19, 637-655. https://doi.org/10.1038/s41571-022-00671-9
  32. Qiao, J. T., Cui, C., Qing, L., Wang, L. S., He, T. Y., Yan, F., Liu, F. Q., Shen, Y. H., Hou, X. G. and Chen, L. (2018) Activation of the STING-IRF3 pathway promotes hepatocyte inflammation, apoptosis and induces metabolic disorders in nonalcoholic fatty liver disease. Metabolism 81, 13-24. https://doi.org/10.1016/j.metabol.2017.09.010
  33. Qin, Z., Ljubimov, V. A., Zhou, C., Tong, Y. and Liang, J. (2016) Cell-free circulating tumor DNA in cancer. Chin. J. Cancer 35, 36. https://doi.org/10.1186/s40880-016-0092-4
  34. Rizwan, H., Pal, S., Sabnam, S. and Pal, A. (2020) High glucose augments ROS generation regulates mitochondrial dysfunction and apoptosis via stress signalling cascades in keratinocytes. Life Sci. 241, 117148. https://doi.org/10.1016/j.lfs.2019.117148
  35. Schulze, S., Stoss, C., Lu, M., Wang, B., Laschinger, M., Steiger, K., Altmayr, F., Friess, H., Hartmann, D., Holzmann, B. and Huser, N. (2018) Cytosolic nucleic acid sensors of the innate immune system promote liver regeneration after partial hepatectomy. Sci. Rep. 8, 12271. https://doi.org/10.1038/s41598-018-29924-3
  36. Shinobu, N., Iwamura, T., Yoneyama, M., Yamaguchi, K., Suhara, W., Fukuhara, Y., Amano, F. and Fujita, T. (2002) Involvement of TIRAP/MAL in signaling for the activation of interferon regulatory factor 3 by lipopolysaccharide. FEBS Lett. 517, 251-256. https://doi.org/10.1016/S0014-5793(02)02636-4
  37. Singh, K., Deshpande, P., Li, G., Yu, M., Pryshchep, S., Cavanagh, M., Weyand, C. M. and Goronzy, J. J. (2012) K-RAS GTPase- and B-RAF kinase-mediated T-cell tolerance defects in rheumatoid arthritis. Proc. Natl. Acad. Sci. U. S. A. 109, E1629-E1637. https://doi.org/10.1073/pnas.1117640109
  38. Stewart, M. (2007) Molecular mechanism of the nuclear protein import cycle. Nat. Rev. Mol. Cell Biol. 8, 195-208. https://doi.org/10.1038/nrm2114
  39. Takahama, M., Fukuda, M., Ohbayashi, N., Kozaki, T., Misawa, T., Okamoto, T., Matsuura, Y., Akira, S. and Saitoh, T. (2017) The RAB2B-GARIL5 complex promotes cytosolic DNA-induced innate immune responses. Cell Rep. 20, 2944-2954. https://doi.org/10.1016/j.celrep.2017.08.085
  40. Van Acker, T., Eyckerman, S., Vande Walle, L., Gerlo, S., Goethals, M., Lamkanfi, M., Bovijn, C., Tavernier, J. and Peelman, F. (2014) The small GTPase Arf6 is essential for the Tram/Trif pathway in TLR4 signaling. J. Biol. Chem. 289, 1364-1376. https://doi.org/10.1074/jbc.M113.499194
  41. Xu, D., Tian, Y., Xia, Q. and Ke, B. (2021) The cGAS-STING pathway: novel perspectives in liver diseases. Front. Immunol. 12, 682736. https://doi.org/10.3389/fimmu.2021.682736
  42. Yang, S., Imamura, Y., Jenkins, R. W., Canadas, I., Kitajima, S., Aref, A., Brannon, A., Oki, E., Castoreno, A., Zhu, Z., Thai, T., Reibel, J., Qian, Z., Ogino, S., Wong, K. K., Baba, H., Kimmelman, A. C., Pasca Di Magliano, M. and Barbie, D. A. (2016) Autophagy inhibition dysregulates TBK1 signaling and promotes pancreatic inflammation. Cancer Immunol. Res. 4, 520-530. https://doi.org/10.1158/2326-6066.CIR-15-0235
  43. Yang, Y. K., Qu, H., Gao, D., Di, W., Chen, H. W., Guo, X., Zhai, Z. H. and Chen, D. Y. (2011) ARF-like protein 16 (ARL16) inhibits RIG-I by binding with its C-terminal domain in a GTP-dependent manner. J. Biol. Chem. 286, 10568-10580. https://doi.org/10.1074/jbc.M110.206896
  44. Yoneyama, M., Kikuchi, M., Natsukawa, T., Shinobu, N., Imaizumi, T., Miyagishi, M., Taira, K., Akira, S. and Fujita, T. (2004) The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5, 730-737. https://doi.org/10.1038/ni1087
  45. Zhang, B., Li, M., Chen, L., Yang, K., Shan, Y., Zhu, L., Sun, S., Li, L. and Wang, C. (2009) The TAK1-JNK cascade is required for IRF3 function in the innate immune response. Cell Res. 19, 412-428. https://doi.org/10.1038/cr.2009.8