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Title: Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs

Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Altogether, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.
Authors:
 [1] ;  [2] ;  [2] ;  [3] ;  [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [2]
  1. Argonne National Lab. (ANL), Argonne, IL (United States)
  2. Univ. of California, Santa Barbara, CA (United States)
  3. Univ. of California, Irvine, CA (United States)
  4. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
Publication Date:
Grant/Contract Number:
AC02-06CH11357
Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: 17; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Research Org:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; immunity; peptide elongation factor tu; transfer rna; toxins; nuclease
OSTI Identifier:
1393513

Michalska, Karolina, Gucinski, Grant C., Garza-Sanchez, Fernando, Johnson, Parker M., Stols, Lucy M., Eschenfeldt, William H., Babnigg, Gyorgy, Low, David A., Goulding, Celia W., Joachimiak, Andrzej, and Hayes, Christopher S.. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs. United States: N. p., Web. doi:10.1093/nar/gkx700.
Michalska, Karolina, Gucinski, Grant C., Garza-Sanchez, Fernando, Johnson, Parker M., Stols, Lucy M., Eschenfeldt, William H., Babnigg, Gyorgy, Low, David A., Goulding, Celia W., Joachimiak, Andrzej, & Hayes, Christopher S.. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs. United States. doi:10.1093/nar/gkx700.
Michalska, Karolina, Gucinski, Grant C., Garza-Sanchez, Fernando, Johnson, Parker M., Stols, Lucy M., Eschenfeldt, William H., Babnigg, Gyorgy, Low, David A., Goulding, Celia W., Joachimiak, Andrzej, and Hayes, Christopher S.. 2017. "Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs". United States. doi:10.1093/nar/gkx700. https://www.osti.gov/servlets/purl/1393513.
@article{osti_1393513,
title = {Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs},
author = {Michalska, Karolina and Gucinski, Grant C. and Garza-Sanchez, Fernando and Johnson, Parker M. and Stols, Lucy M. and Eschenfeldt, William H. and Babnigg, Gyorgy and Low, David A. and Goulding, Celia W. and Joachimiak, Andrzej and Hayes, Christopher S.},
abstractNote = {Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Altogether, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.},
doi = {10.1093/nar/gkx700},
journal = {Nucleic Acids Research},
number = 17,
volume = 45,
place = {United States},
year = {2017},
month = {8}
}