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Scripps Laboratories for tRNA Synthetase Research


Complete Publication List of Xiang-Lei Yang, Ph.D.

75.  Xu, X., Zhou, H., Zhou, Q., Hong, F., Vo, MN, Niu, W., Wang, Z., Xiong, X., Nakamura, K., Wakasugi, K., Schimmel, P., Yang, XL. (2017) An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function. RNA  Biol. Sep 14:1-10. doi: 10.1080/15476286.2017.1377868

74.  Blocquel, D., Li, S., Wei, N., Daub, H., Sajish, M., Erfurth, M-L., Kooi, G., Zhou, J., Bai, G., Schimmel, P., Jordanova, A., Yang, X.L. (2017) Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.  Nucleic Acids Res.45:8091-8104.

73. Sleigh, J.N., Dawes, J.M., West, S.J., Wei, N., Spaulding, E.L., Gómez-Martín, A., Zhang, Q., Burgess, R.W., Cader, M.Z., Talbot, K., Yang, X.L., Bennett, D.L., Schiavo, G. (2017) Trk receptor signaling and sensory neuron fate are perturbed in human neuropathy caused by Gars mutations. Proc. Natl. Acad. Sci. U S A 114:E3324-E3333.

72.  Atkinson, D., Nikodinovic Glumac, J., Asselbergh, B., Ermanoska, B., Blocquel, D., Steiner, R., Estrada-Cuzcana, A., Peeters, K., Ooms, T., De Vriendt, E., Yang, X-L., Hornemann, T., Milic Rasic, V., Jordanova, A. (2017) Sphingosine 1-phosphate lyase deficiency causes Charcot-Marie-Tooth neuropathy.  Neurology 88:533-542.

71. Shi, Y., Wei. N., Yang, X-L. (2017). Studying nuclear functions of aminoacyl tRNA synthetases. Methods 113:105-110.

70. Sun, L., Song, Y., Blocquel, D., Yang, X-L., and Schimmel, P. (2016). Two crystal structures reveal design for repurposing the C-Ala domain of human AlaRS. Proc Natl Acad Sci U.S.A.  113: 14300-14305

69. Sun L., Gomes, AC., He, W., Zhou, H., Wang, X., Pan, DW., Schimmel, Pan, T., Yang, X-L. (2016). Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 base pair. J. Am Chem Soc. 138: 12948-12955.

68. Mo, Z., Zhang, Q., Lauer, J., Shi, Y., Sun, L., Griffin, P.R., Yang, X-L. (2016). Neddylation requires glycyl-tRNA synthetase to protect activated E2.  Nat. Struct. Mol. Biol. 23:730-737.

67. Wei, Z., Xu, Z., Lo, W.S., Ye, F., Lau, C.F., Wang, F., Zhou, J.J., Nangle, L.A., Yang, X-L., Zhang M., Schimmel, P. (2016) Alternative splicing creates two new architectures for human tyrosyl-tRNA synthetase. Nuclei Acids Res. 44: 1247-1255.

66. He, W., Bai, G., Zhou, H., Wei, N., White, M. N., Lauer, J., Liu, H., Shi, Y., Dumitru, C. D., Lettieri, K., Shubayev, V., Jordanova, A., Guergueltcheva, V., Griffin, P. L., Burgess, R. W., Pfaff, S. L., and Yang, X.-L. (2015). CMT2D neuropathy is linked to the neomorphic binding activity of glycyl-tRNA synthetase. Nature 526: 710-714.

65. Niehues, S., Bussmann, J., Steffes, G., Erdmann, I., Kohrer, C., Sun, L., Wagner, M., Schafer, K., Wang, G., Koerdt, S. N., Stum, M., RajBhandary, U. L., Thomas, U., Aberle, H., Burgess, R. W., Yang, X.-L., Dieterich, D., and Storkebaum, E. (2015). Impaired protein translation in Drosophila models for Charcot-Marie-Tooth neuropathy caused by mutant tRNA synthetases. Nat. Commun. 6: 7520.

64. Yang, X.-L. (2014). tRNA-derived G-quadruplex protects motor neurons. Proc. Natl. Acad. Sci. U S A. 111: 18108-18109.

63. Wei, N., Shi, Y., Truong, L. N., Fisch, K. M., Xu, T., Gardiner, E., Fu, G., Hsu, Y. S., Kishi, S., Su, A. I., Wu, X., and Yang, X.-L. (2014). Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage. Mol. Cell 56: 323-332.

62. Ishimura, R., Nagy, G., Dotu, I., Zhou, H., Yang, X.-L., Schimmel, P,. Senju, S., Nishimura, Y., Chuang. J. H., and Ackerman, S. L. (2014). Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 345: 455-459.

61. Lo, W.-S., Gardiner, E., Xu, Z., Lau, C.-F., Wang, F., Zhou, J. J., Mendlein, J. D., Nangle, L. A., Chiang, K. P., Yang, X.-L., Au, K.-F., Wong, W. H., Guo, M., Zhang, M., and Schimmel, P. (2014). Human tRNA synthetase catalytic nulls with diverse functions. Science 345: 328-332.

60. Naganuma, M., Sekine, S., Chong, Y. E., Guo, M., Yang, X.-L., Gamper, H., Hou, Y.-M., Schimmel, P., and Yokoyama, S. (2014). The selective tRNA aminoacylation mechanism based on a single G·U pair. Nature 510: 507-511.

59. Shi, Y., Xu, X., Zhang, Q., Fu, G., Mo, Z., Wang, G. S., Kishi, S., and Yang, X.-L.* (2014). tRNA synthetase counteracts c-Myc to develop functional vasculature. eLife 3: e02349. (*Corresponding author).

58. Zhou, M. J., Wang, F., Xu, Z., Lo, W.-S., Lau, C.-F., Chiang, K. P., Nangle, L. A., Ashlock, M. A., Mendlein, J. D., Yang, X.-L., Zhang, M., and Schimmel, P. (2014). Secreted histidyl-tRNA synthetase splice variants elaborate major epitopes for autoantibodies in inflammatory myositis. J. Biol. Chem. 289: 19269-19275.

57. Yang, X.-L. (2013). Structural disorder in expanding the functionome of aminoacyl-tRNA synthetases. Chem. Biol. 20: 1093-1099.

56. Guo, M. and Yang, X.-L. (2014). Architecture and metamorphosis. Top. Curr. Chem. 344: 89–118. (Epub 2013).

55. Wang, F., Xu, Z., Zhou, J. J., Lo, W. S., Lau, C. F., Nangle, L. A., Yang, X.-L., Zhang, M., and Schimmel, P. (2013). Regulated capture by exosomes of mRNAs for cytoplasmic tRNA synthetases. J. Biol. Chem. 288: 29223-29228.

54. Xu, X., Shi, Y., and Yang, X.-L.* (2013). Crystal structure of human seryl-tRNA synthetase and Ser-SA complex reveals a molecular lever specific to higher eukaryotes. Structure 21: 2078-2086 (*Corresponding author).

53. Gonzalez, M., McLaughlin, H., Houlden, H., Guo, M., Yo-Tsen, L., Hadjivassilious, M., Speziani, F., Yang, X.-L., Antonellis, A., Reilly, M..M., and Züchner, S. (2013). Exome sequencing identifies a significant variant in methionyl-tRNA synthetase (MARS) in a family with late-onset CMT2. J. Neurol. Neurosurg. Psychiatry 84: 1247-1249.

52. Zhou, H., Sun, L., Yang, X.-L., and Schimmel, P. (2013). ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase. Nature 494: 121–124.

51. Ofir-Birin, Y., Fang, P., Bennett, S. P., Zhang, H.-M., Wang, J., Rachmin, I., Shapiro, R., Song, J., Dagan, A., Pozo, J., Kim, S., Marshall, A. G., Schimmel, P., Yang, X.-L., Nechushtan, H., Razin, E., and Guo, M. (2013). Structural switch of lysyl-tRNA synthetase between translation and transcription. Mol. Cell 49: 30–42.

50. Xu, Z., Wei, Z., Zhou, J. J., Ye, F., Lo, W. S., Wang, F., Lau, C. F., Wu, J., Nangle, L. A., Chiang, K. P., Yang, X.-L., Zhang, M., and Schimmel, P. (2012). Internally deleted human tRNA synthetase suggests evolutionary pressure for repurposing. Structure 20: 1470–1477.

49. Lee, P. S., Zhang, H.-M., Marshall, A. G., Yang, X.-L., and Schimmel, P. (2012). Uncovering of a short internal peptide activates a tRNA synthetase procytokine. J. Biol. Chem. 287: 20504-20508.

48. Mathew, S., Zhou, Q., Kishi, S., Valdez Jr, D. M., Kapoor, M., Guo, M., Lee, S., Kim, S., Yang, X.-L., and Schimmel, P. (2012). Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-γ and p53 signaling. Nat. Chem. Biol. 8: 547-554.

47. Park, M. C., Kang, T., Jin, D., Han, J. M., Kim, S. B., Park, Y. J., Cho, K., Park, Y. W., Guo, M., He, W., Yang, X.-L., Schimmel, P., and Kim, S. (2012). Secreted human glycyl-tRNA synthetase implicated in defense against ERK-activated tumorigenesis. Proc. Natl. Acad. Sci. U S A. 109: E640-647.

46. Xu, X., Shi, Y., Zhang, H.-M., Swindell, E. C., Marshall, A. G., Guo, M., Kishi, S., and Yang, X.-L.* (2012). Unique domain appended to vertebrate tRNA synthetase is essential for vascular development. Nat. Commun. 3: 681. (*Corresponding author).

45. Fu, G., Xu, T., Shi, Y., Wei, N., Yang, X.-L.* (2012). tRNA-controlled nuclear import of a human tRNA synthetase. J. Biol. Chem. 287: 9330-9334. (*Corresponding author).

44. Motley, W. W., Seburn, K. L., Nawaz, M. H., Miers, K. E., Cheng, J., Antonellis, A., Green, E. D., Talbot, K., Yang, X.-L., Fischbeck, K. H., and Burgess, R. W. (2011). Charcot-Marie-Tooth-linked mutant GARS is toxic to peripheral neurons independent of wild-type GARS levels. PLoS Genet. 7: e1002399.

43. Yang, X.-L.* and Schimmel, P. (2011). Functional expansion of the tRNA world under stress. Mol. Cell 43: 500-502. (*Corresponding author).

42. He, W., Zhang, H.-M., Chong, Y. E., Guo, M., Marshall, A. G., and Yang, X.-L.* (2011). Dispersed disease-causing neomorphic mutations on a single protein promote the same localized conformational opening. Proc. Natl. Acad. Sci. U S A. 108: 12307-12312. (*Corresponding author).

41. Fang, P., Zhang, H.-M., Shapiro, R., Marshall, A. G., Schimmel, P., Yang, X.-L.*, and Guo, M. (2011). Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex. Proc. Natl. Acad. Sci. U S A. 108: 8239-8244. (*Co-corresponding author).

40. Nawaz, M. H., Merriman, E., Yang, X.-L., and Schimmel, P. (2011). p23H implicated as cis/trans regulator of AlaXp-directed editing for mammalian cell homeostasis. Proc. Natl. Acad. Sci. U S A. 108: 2723-2728.

39. Vo, M. N., Yang, X.-L.* and Schimmel, P. (2011). Dissociating quaternary structure regulates cell-signaling functions of a secreted human tRNA synthetase. J. Biol. Chem. 286: 11563-11568. (*Co-corresponding author).

38. Guo, M., Shapiro, R., Morris, G. M., Yang, X.-L., and Schimmel, P. (2010). Packaging HIV virion components through dynamic equilibria of a human tRNA synthetase. J. Phys. Chem. 114: 16273-16279.

37. Han, G. W., Yang, X.-L., et al. (2010). Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66: 1326-1334.

36. Guo, M., Yang, X.-L. and Schimmel, P. (2010). New functions of aminoacyl-tRNA synthetases beyond translation. Nat. Rev. Mol. Cell Biol. 11: 668-674.

35. Guo, M., Shapiro, R., Schimmel, P. and Yang, X.-L.* (2010). Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase. Acta Crystallogr. D Biol. Crystallogr. 66: 243-250. (*Corresponding author).

34. Guo, M., Schimmel, P., and Yang, X.-L.* (2010). Functional expansion of human tRNA synthetases achieved by structural inventions. FEBS Lett. 584: 434-442. (*Corresponding author).

33. Zhou, Q., Kapoor, M., Guo, M., Belani, R., Xu, X., Kiosses, W. B., Hanan M., ParK, C., Armour, E., Do, M.-H., Nangle, L. A., Schimmel, P., and Yang, X.-L.* (2010). Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality. Nat. Struc. Mol. Biol. 17: 57-61. (*Corresponding author).

32. Guo, M., Chong, Y. E., Shapiro, R., Beebe, K., Yang, X.-L., and Schimmel, P. (2009). Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 462: 808-812.

31. Guo, R.-T., Chong, Y. E., Guo, M., and Yang, X.-L.* (2009). Crystal structures and biochemical analyses suggest a unique mechanism and role for human glycl-tRNA synthetase in Ap4A homeostasis. J. Biol. Chem. 284: 28968-28976. (*Corresponding author).

30. Guo, M., Chong, Y. E., Beebe, K., Shapiro, R., Yang, X.-L., and Schimmel, P. (2009). The C-Ala domain brings together editing and aminoacylation functions on one tRNA. Science 325: 744-747.

29. Storkebaum, E., Leitão-Gonçalves, R., Godenschwege, T., Nangle, L., Mejia, M., Bosmans, I., Ooms, T., Jacobs, A., Van Dijck, P., Yang, X.-L., Schimmel, P., Norga, K., Timmerman, V., Callaerts, P., and Jordanova, A. (2009). Dominant mutations in the tyrosyl-tRNA synthetase gene recapitulate in Drosophila features of human Charcot-Marie-Tooth neuropathy. Proc. Natl. Acad. Sci. U S A. 106: 11782-11787.

28. Kapoor, M., Otero, F. J., Slike, B. M., Ewalt, K. L., and Yang, X.-L.* (2009). Mutational separation of aminoacylation and cytokine activities of human tyrosyl-tRNA synthetase. Chem. Biol. 16: 531–539. (*Corresponding author).

27. Chong, Y. E., Yang, X.-L., and Schimmel, P. (2008). Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation. J. Biol. Chem. 283: 30073-30078.

26. Cheng, G., Zhang, H., Yang X.-L., Tzima, E., Ewalt, K. L., Schimmel, P., and Faber, J. E. (2008). Effect of mini-tyrosyl-tRNA synthetase on ischemic angiogenesis, leukocyte recruitment and vascular permeability. Am. J. Physiol. Regul. Integr. Comp. Physiol. 295: R1138-1146.

25. Guo, M., Ignatov, M., Musier-Forsyth, K., Schimmel, P., and Yang, X.-L.* (2008). Crystal structure of tetrameric form of human lysyl-tRNA synthetase: Implications for multisynthetase complex formation. Proc. Natl. Acad. Sci. U S A. 105: 2331-2336. (*Corresponding author).

24. Greenberg, Y., Kiosses, W. B., Ewalt, K., Yang, X.-L., Schimmel, P., Reader, J. S., and Tzima, E. (2008). The novel fragment of tyrosyl tRNA synthetase, mini-TyrRS, is secreted to induce an angiogenic response in endothelial cells. FASEB J. 22: 1597-1605.

23. Kapoor, M., Zhou, Q., Otero, F., Myers, C. A., Bates, A., Belani, R., Liu, J., Luo, J. K., Tzima, E., Zhang, D.-E., Yang, X.-L., and Schimmel P. (2008). Evidence for annexin II/S100A10 complex and plasmin in mobilization of cytokine activity of human TrpRS. J. Biol. Chem. 283: 2070-2077.

22. Yang, X.-L.*, Kapoor, M., Otero, F. J., Slike, B. Tsuruta, H., Frausto, R., Bates, A., Ewalt, K. L., Cheresh, D. A., and Schimmel, P. (2007). Gain-of-function mutational activation of human tRNA synthetase procytokine. Chem. Biol. 14: 1323-1333. (*Corresponding author).

21. Nangle, L. A., Zhang, W., Xie, W., Yang, X.-L.,* and Schimmel, P. (2007). Charcot-Marie-Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect. Proc. Natl. Acad. Sci. U S A. 104: 11239-11244. (*Co-corresponding author).

20. Xie, W., Nangle, L. A., Zhang, W., Schimmel, P., and Yang, X.-L.* (2007). Long-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase. Proc. Natl. Acad. Sci. U S A. 104: 9976-9981. (*Co-corresponding author).

19. Yang, X.-L.*, Guo, M., Kapoor, M., Ewalt, K. L., Otero, F. J., Skene, R. J., McRee, D. E., and Schimmel, P. (2007). Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase. Structure 15: 793-805. (*Corresponding author).

18. Schimmel, P. and Yang, X.-L. (2006). Perfecting the genetic code with an RNP complex. Structure 14: 1729-1730.

17. Xie, W., Schimmel, P., and Yang, X.-L.* (2006). Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot-Marie-Tooth disease. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62: 1243-1246. (*Corresponding author).

16. Yang, X.-L.*, Otero, F. J. , Ewalt, K. L., Liu, J., Swairjo, M. A., Kohrer, C., RajBhandary, U. L., Skene, R. J., McRee, D. E., and Schimmel, P. (2006). Two conformations of a crystalline human tRNA synthetase-tRNA complex: Implications for protein synthesis. EMBO J. 25: 2919-2929. (*Corresponding author).

15. Ewalt, K. L., Yang, X.-L., Otero, F. J., Liu, J., Slike, B., and Schimmel, P. (2005). Variant of human enzyme sequesters reactive intermediate. Biochemistry 44: 4216-4221.

14. Schimmel, P. and Yang, X.-L. (2004). Two classes give lessons about CCA. Nat. Struct. Mol. Biol. 11: 807-808.

13. Yang, X.-L., Schimmel, P., and Ewalt, K. L. (2004). Relationship of two human tRNA synthetases used in cell signaling. Trends Biochem. Sci. 29: 250-256.

12. Swairjo, M. A., Otero, F. J., Yang, X.-L., Lovato, M. A., Skene, R. J., McRee, D. E., Ribas de Pouplana, L., and Schimmel, P. (2004). Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Mol. Cell 13: 829-841.

11. Yang, X.-L., Otero, F. J. , Skene, R. J., McRee, D. E., Schimmel, P., and Ribas de Pouplana, L. (2003). Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains. Proc. Natl. Acad. Sci. U S A. 100: 15376-15380.

10. Yang, X.-L, Liu, J., Skene, R. J., McRee, D. E., and Schimmel, P. (2003). Crystal structure of an EMAP-II-like cytokine released from a human tRNA synthetase. Helv. Chim. Acta. 86: 1246-1257.

9. Liu, J., Yang, X.-L, Ewalt, K. L., and Schimmel, P. (2002). Mutational switching of a yeast tRNA synthetase into a mammalian-like synthetase cytokine. Biochemistry 41: 14232-14237.

8. Yang, X.-L., Skene, R. J., McRee, D. E., and Schimmel, P. (2002). Crystal structure of a human aminoacyl-tRNA synthetase cytokine. Proc. Natl. Acad. Sci. U S A. 99: 15369-15374.

7. Robinson, H., Gao, Y.-G., Yang, X.-L., Sanishvili, R., Joachimiak, A., and Wang, A. H.-J. (2001). Crystallographic analysis of a novel complex of actinomycin D bound to the DNA decamer CGATCGATCG. Biochemistry 40: 5587-5592.

6. Yang, X.-L., Robinson H, Gao, Y.-G., and Wang, A. H.-J. (2000). Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms. Biochemistry 39: 10950-10957.

5. Yang, X.-L., Hubbard IV, R. B., Lee, M., Tao, Z.-F., Sugiyama, H., and Wang, A. H.-J. (1999). Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs. Nucleic Acids Res. 27: 4183-4190.

4. Yang, X.-L. and Wang, A. H.-J. (1999). Structural studies of atom-specific anticancer drugs acting on DNA. Pharmacol. Ther. 83: 181-215.

3. Yang, X.-L., Kaenzig, C., Lee, M., and Wang, A. H.-J. (1999). Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy. Eur. J. Biochem. 263: 646-655.

2. Yang, X.-L., Sugiyama, H., Ikeda, S., Saito, I., and Wang, A. H.-J. (1998). Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. Biophysical J. 75: 1163-1171.

1. Yang, X.-L. and Wang, A. H.-J. (1997). Structural analysis of Z-Z DNA junctions with A:A and T:T mismatched base pairs by NMR. Biochemistry 36: 4258-4267.


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