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Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex

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Abstract

The evolutionary necessity of aminoacyl-tRNA synthetases being associated into complex is unknown. Human lysyl-tRNA synthetase (LysRS) is one component of the multi-tRNA synthetase complex (MSC), which is not only critical for protein translation but also involved in multiple cellular pathways such as immune response, cell migration, etc. Here, combined with crystallography, CRISPR/Cas9-based genome editing, biochemistry, and cell biology analyses, we show that the structures of LysRSs from metazoan are more dynamic than those from single-celled organisms. Without the presence of MSC scaffold proteins, such as aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2), human LysRS is free from the MSC. The interaction with AIMP2 stabilizes the closed conformation of LysRS, thereby protects the essential aminoacylation activity under stressed conditions. Deleting AIMP2 from the human embryonic kidney 293 cells leads to retardation in cell growth in nutrient deficient mediums. Together, these results suggest that the evolutionary emergence of the MSC in metazoan might be to protect the aminoacyl-tRNA synthetase components from being modified or recruited for use in other cellular pathways.

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Atomic coordinates and structure factors for the reported crystal structures have been deposited with the Protein Data bank under accession number 5YZX and 7F6W. Other data supporting the findings of this study are available from the corresponding author on reasonable request.

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Acknowledgements

We thank Dr. K. Musier-Forsyth for her helpful comments and revision of the manuscript. And we gratefully acknowledge help from staffs of beamline 17U1 at Shanghai Synchrotron Radiation Facility.

Funding

This work was supported by the National Natural Science Foundation of China grants 21977107, 21778064, 21778067, 21977108, 31822015, 81870896, 31670801; the Strategic Priority Research Program of the Chinese Academy of Sciences grant XDB20000000; the CAS President's International Fellowship Initiative (PIFI); a 1000-talent young investigator award; a 100-talent program of the Chinese Academy of Sciences; and the State Key Laboratory of Bioorganic and Natural Products Chemistry.

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  1. Hamid Ali

    Present address: Department of Biosciences, COMSATS University Islamabad, Islamabad, 44000, Pakistan

  2. Siqi Wu and Li Zheng contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China

    Siqi Wu, Li Zheng, Zhoufei Hei, Peifeng Li, Jiayuan Wang, Hamid Ali, Jing Wang & Pengfei Fang

  2. School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China

    Li Zheng, Jing Wang & Pengfei Fang

  3. State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China

    Jing-Bo Zhou, Guang Li & Xiao-Long Zhou

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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Siqi Wu, Li Zheng, Zhoufei Hei, Jing-Bo Zhou, Guang Li, Peifeng Li, Jiayuan Wang, and Hamid Ali. The first draft of the manuscript was written by Siqi Wu and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Wu, S., Zheng, L., Hei, Z. et al. Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex. Cell. Mol. Life Sci. 79, 128 (2022). https://doi.org/10.1007/s00018-022-04158-9

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