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A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase

Nature Structural & Molecular Biology volume 11, pages 149–156 (2004)Cite this article

Abstract

Human tryptophanyl-tRNA synthetase (TrpRS) is secreted into the extracellular region of vascular endothelial cells. The splice variant form (mini TrpRS) functions in vascular endothelial cell apoptosis as an angiostatic cytokine. In contrast, the closely related human tyrosyl-tRNA synthetase (TyrRS) functions as an angiogenic cytokine in its truncated form (mini TyrRS). Here, we determined the crystal structure of human mini TrpRS at a resolution of 2.3 Å and compared the structure with those of prokaryotic TrpRS and human mini TyrRS. Deletion of the tRNA anticodon-binding (TAB) domain insertion, consisting of eight residues in the human TrpRS, abolished the enzyme's apoptotic activity for endothelial cells, whereas its translational catalysis and cell-binding activities remained unchanged. Thus, we have identified the inserted peptide motif that activates the angiostatic signaling.

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Figure 1: Structure of the human mini TrpRS structure.
Figure 2: Structural comparison.
Figure 3: In vitro apoptotic activities and housekeeping translational activities of TrpRS mutants.
Figure 4: Angiogenesis assay in chick CAM.
Figure 5: Binding of the TrpRS deletion mutants to BAECs.
Figure 6: The effect of the YGY sequence mutation on the proliferation of BAECs and cell binding.

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References

  1. Ibba, M. & Soll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69, 617–650 (2000).

    Article  CAS  Google Scholar 

  2. Martinis, S.A., Plateau, P., Cavarelli, J. & Florentz, C. Aminoacyl-tRNA synthetases: a family of expanding functions. EMBO J. 18, 4591–4596 (1999).

    Article  CAS  Google Scholar 

  3. Ko, Y.G., Park, H. & Kim, S. Novel regulatory interactions and activities of mammalian tRNA synthetases. Proteomics 2, 1304–1310 (2002).

    Article  CAS  Google Scholar 

  4. Ko, Y.G. et al. Glutamine-dependent antiapoptotic interaction of human glutaminyl-tRNA synthetase with apoptosis signal-regulating kinase 1. J. Biol. Chem. 276, 6030–6036 (2001).

    Article  CAS  Google Scholar 

  5. Kisselev, L.L. & Wolfson, A.D. Aminoacyl-tRNA synthetases from higher eukaryotes. Prog. Nucleic Acids Res. Mol. Biol. 48, 83–142 (1994).

    Article  CAS  Google Scholar 

  6. Doublie, S., Bricogne, G., Glimore, C. & Carter, C. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 3, 17–31 (1995).

    Article  CAS  Google Scholar 

  7. Jeong, E.S. et al. Structural analysis of peptide motifs in human bifunctional tRNA synthetase: identification of RNA-binding residues and functional implications for tandem repeats. Biochemistry 39, 15775–15782 (2000).

    Article  CAS  Google Scholar 

  8. Hirakata, M. et al. Autoantibodies to glycyl-transfer RNA synthetase in myositis. Association with dermatomyositis and immunologic heterogeneity. Arthritis Rheum. 39, 146–151 (1996).

    Article  CAS  Google Scholar 

  9. Lemaire, G., Gros, C., Epely, S., Kaminsky, M. & Labouesse, B. Multiple forms of tryptophanyl-tRNA synthetase from beef pancreas. Eur. J. Biochem. 51, 237–252 (1975).

    Article  CAS  Google Scholar 

  10. Sallafranque, M.L. et al. Tryptophanyl-tRNA synthetase is a major soluble protein species in bovine pancreas. Biochem. Biophys. Acta 882, 192–199 (1986).

    Article  CAS  Google Scholar 

  11. Favorova, O.O., Zargarova, T.A., Rukosuyev, V.S., Beresten, S.F. & Kisselev, L.L. Molecular and cellular studies of tryptophanyl-tRNA synthetases using monoclonal antibodies: remarkable variations in the content of tryptophanyl-tRNA synthetase in the pancreas of different mammals. Eur. J. Biochem. 184, 583–588 (1989).

    Article  CAS  Google Scholar 

  12. Kisselev, L.L. Mammalian tryptophanyl-tRNA synthetases. Biochimie 75, 1027–1039 (1993).

    Article  CAS  Google Scholar 

  13. Wakasugi, K. & Schimmel, P. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science 284, 147–151 (1999).

    Article  CAS  Google Scholar 

  14. Wakasugi, K. et al. Induction of angiogenesis by a fragment of human tyrosyl-tRNA synthetase. J. Biol. Chem. 277, 20124–20126 (2002).

    Article  CAS  Google Scholar 

  15. Tolstrup, A.B., Bejder, A., Fleckner, J. & Justesen, J. Transcriptional regulation of the interferon-γ-inducible tryptophanyl-tRNA synthetase induces alternative splicing. J. Biol. Chem. 270, 397–403 (1995).

    Article  CAS  Google Scholar 

  16. Wakasugi, K. et al. Human aminoacyl-tRNA synthetase as a regulator of angiogenesis. Proc. Natl. Acad. Sci. USA 99, 173–177 (2002).

    Article  CAS  Google Scholar 

  17. Kisselev, L., Frolova, L. & Haenni, A.L. Interferon inducibility of mammalian tryptophanyl-tRNA synthetase: new perspectives. Trends Biochem. Sci. 18, 263–267 (1993).

    Article  CAS  Google Scholar 

  18. Shaw, A.C. et al. Mapping and identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 20, 984–993 (1999).

    Article  CAS  Google Scholar 

  19. Otani, A. et al. A fragment of human TrpRS as a potent antagonist of ocular angiogenesis. Proc. Natl. Acad. Sci. USA 99, 178–183 (2002).

    Article  CAS  Google Scholar 

  20. Ewalt, K.L. & Schimmel, P. Activation of angiogenic signaling pathways by two human tRNA synthetases. Biochemistry 41, 13344–13349 (2002).

    Article  CAS  Google Scholar 

  21. Yang, X.L., Skene, R., McRee, D.E. & Schimmel, P. Crystal structure of a human aminoacyl-tRNA synthetase cytokine. Proc. Natl. Acad. Sci. USA 99, 15369–15374 (2002).

    Article  CAS  Google Scholar 

  22. Yaremchuk, A., Kriklivyi, I., Tukalo, M. & Cusack, S. Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J. 21, 3829–3840 (2002).

    Article  CAS  Google Scholar 

  23. Kobayashi, T. et al. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat. Struct. Biol. 10, 425–432 (2003).

    Article  CAS  Google Scholar 

  24. Jia, J. et al. Two essential regions for tRNA recognition in Bacillus subtilis tryptophanyl-tRNA synthetase. Biochem. J. 365, 749–756 (2002).

    Article  CAS  Google Scholar 

  25. Raben, N. et al. A motif in human histidyl-tRNA synthetase which is shared among several aminoacyl-tRNA synthetases is a coiled-coil that is essential for enzymatic activity and contains the major autoantigenic epitope. J. Biol. Chem. 269, 24277–24283 (1994).

    CAS  PubMed  Google Scholar 

  26. Park, S.G. et al. Dose-dependent biphasic activity of tRNA synthetase-associating factor, p43, in angiogenesis. J. Biol. Chem. 277, 45243–45248 (2002).

    Article  CAS  Google Scholar 

  27. Booth, V., Keizer, D.W., Kamphuis, M.B., Clark-Lewis, I. & Sykes, B.D. The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions. Biochemistry 41, 10418–10425 (2002).

    Article  CAS  Google Scholar 

  28. Romagnani, P. et al. Cell cycle-dependent expression of CXC chemokine receptor 3 by endothelial cells mediates angiostatic activity. J. Clin. Invest. 107, 53–63 (2001).

    Article  CAS  Google Scholar 

  29. Otani, A. et al. Bone marrow–derived stem cells target retinal astrocytes and can promote or inhibit retinal angiogenesis. Nat. Med. 8, 1004–1010 (2002).

    Article  CAS  Google Scholar 

  30. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  31. Weeks, C.M. & Miller, R. The design and implementation of SnB version 2.0. J. Appl. Crystallogr. 32, 120–124 (1999).

    Article  CAS  Google Scholar 

  32. Collaborative Computational Project, Number 4. CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

  33. Terwilliger, T.C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965–972 (2000).

    Article  CAS  Google Scholar 

  34. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  35. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank M. Ibba (Ohio State University) for helpful discussions during the manuscript preparation. We also thank M. Kawamoto and H. Sakai (Japanese Synchrotron Radiation Research Institute (JASRI)) for their help in data collection at SPring-8. This work was supported by a PRESTO Program grant from Japan Science and Technology and a Naito Foundation grant to O.N., and by a grant for National Creative Research Initiatives from the Ministry of Science and Technology, Korea to S.K.

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Authors and Affiliations

  1. Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Yoshiaki Kise, Toru Sengoku, Ryohei Ishii & Shigeyuki Yokoyama

  2. National Creative Research Initiatives Center for ARS Network, College of Pharmacy, Seoul National University, Seoul, 145-742, Korea

    Sang Won Lee, Sang Gyu Park & Sunghoon Kim

  3. Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa, 226-8501, Japan

    Shuya Fukai & Osamu Nureki

  4. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, 230-0045, Yokohama, Japan

    Shigeyuki Yokoyama & Osamu Nureki

  5. PRESTO, Japan Science and Technology,

    Osamu Nureki

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  1. Yoshiaki Kise
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Kise, Y., Lee, S., Park, S. et al. A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase. Nat Struct Mol Biol 11, 149–156 (2004). https://doi.org/10.1038/nsmb722

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