This project focuses on the universal genetic code and how novel components of the apparatus for establishing the code have a role in causing cell and animal pathologies. The work centers on aminoacyl tRNA synthetases and aminoacyl tRNA synthetase-like proteins, and their role in establishing and maintaining the code. The code itself is established in the first reaction of protein synthesis. Here, the 20 aminoacyl tRNA synthetases-one for each amino acid-catalyze the attachments of amino acids to their cognate transfer RNAs. In this reaction, each of the twenty amino acids is matched with the tRNA that contains the anticodon nucleotide triplet (of the code) specifically identified with the particular amino acid. The synthetases, over the long time of evolution, developed other active sites that clear errors of aminoacylation. If not corrected, the mischarged tRNAs insert amino acids at the wrong codons, resulting in mistranslated proteins. Recent work by us and collaborators showed that mistranslation can cause cell and animal pathologies. Throughout evolution, nature has developed genome-encoded fragments of tRNA synthetases that are devoid of aminoacylation activity. Instead of aminoacylation activity, these free-standing fragments are homologs of the editing domains and appear to offer a second route to clearance of errors of misaminoacylation. Thus, errors of aminoacylation can be corrected by the editing domain of the synthetase itself, or by an independently encoded, related fragment that harbors the hydrolytic editing activity. In the coming grant period, much effort is directed at understanding these two systems for preventing mistranslation. These studies emphasize structure-function relationships of a specific tRNA synthetase and its related genome-encoded fragments that have the capacity to clear mischarged tRNA. Preliminary studies suggest that a chosen example-alanyl-tRNA synthetase-has two distinct motifs to capture a specific mischarged tRNA for clearing an error of aminoacylation. One of these is associated with the domain for aminoacylation, while the other is distinct from that domain and is a motif shared with a related genome encoded fragment that clears mischarged alanine tRNAs. Understanding these two distinct mechanisms for tRNA capture is one of several goals. Further work focuses on the problem of how charged tRNA is handled in mammalian cells. In particular, after aminoacylation, we hypothesize that charged tRNA can be 'handed off'or 'channeled'directly to the elongation factor that then goes with its payload to the ribosome. Our work is based on predictions coming from a novel structure of a synthetase-tRNA complex determined recently in this laboratory by x-ray crystallography. These predictions are supported by preliminary biochemical studies. Because channeling can lead to immediate capture of mischarged tRNAs for mistranslation, new challenges are posed for how to prevent cell pathologies in mammals. Collectively, these studies offer a structure function- mechanism effort directed at understanding pathology and disease that can come from errors in the decoding of genetic information, with emphasis on a universal group of proteins (aminoacyl tRNA synthetases) and their natural fragments.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Naganuma, Masahiro; Sekine, Shun-ichi; Chong, Yeeting Esther et al. (2014) The selective tRNA aminoacylation mechanism based on a single G•U pair. Nature 510:507-11
Klipcan, Liron; Safro, Mark; Schimmel, Paul (2013) Anticodon G recognition by tRNA synthetases mimics the tRNA core. Trends Biochem Sci 38:229-32
Zhou, Huihao; Sun, Litao; Yang, Xiang-Lei et al. (2013) ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase. Nature 494:121-4
Sajish, Mathew; Zhou, Quansheng; Kishi, Shuji et al. (2012) Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-? and p53 signaling. Nat Chem Biol 8:547-54
Lee, Peter S; Zhang, Hui-Min; Marshall, Alan G et al. (2012) Uncovering of a short internal peptide activates a tRNA synthetase procytokine. J Biol Chem 287:20504-8
Xu, Zhiwen; Wei, Zhiyi; Zhou, Jie J et al. (2012) Internally deleted human tRNA synthetase suggests evolutionary pressure for repurposing. Structure 20:1470-7
Park, Min Chul; Kang, Taehee; Jin, Da et al. (2012) Secreted human glycyl-tRNA synthetase implicated in defense against ERK-activated tumorigenesis. Proc Natl Acad Sci U S A 109:E640-7
Guo, Min; Schimmel, Paul (2012) Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 22:119-26
Wang, Jing; Fang, Pengfei; Schimmel, Paul et al. (2012) Side chain independent recognition of aminoacyl adenylates by the Hint1 transcription suppressor. J Phys Chem B 116:6798-805
Fang, Pengfei; Zhang, Hui-Min; Shapiro, Ryan et al. (2011) Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex. Proc Natl Acad Sci U S A 108:8239-44

Showing the most recent 10 out of 82 publications