Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei*

  1. Celia W. Goulding‡,**3
  1. From the Departments of ‡Molecular Biology and Biochemistry and
  2. **Pharmaceutical Sciences, University of California at Irvine, Irvine, California 92697,
  3. the §Biomolecular Science and Engineering Program and
  4. Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and
  5. the ‖Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
  1. ↵2 To whom correspondence may be addressed. Tel.: 805-893-2028; E-mail: chayes{at}lifesci.ucsb.edu.
  2. ↵3 To whom correspondence may be addressed. Tel.: 949-824-0337; Fax: 949-824-8551; E-mail: celia.goulding{at}uci.edu.

Abstract

Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition. CDI+ bacteria deploy large CdiA effector proteins, which carry variable C-terminal toxin domains (CdiA-CT). CDI+ cells also produce CdiI immunity proteins that specifically neutralize cognate CdiA-CT toxins to prevent auto-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIE479 toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CTE479 tRNase domain contains a core α/β-fold that is characteristic of PD(D/E)XK superfamily nucleases. Unexpectedly, the closest structural homolog of CdiA-CTE479 is another CDI toxin domain from B. pseudomallei 1026b. Although unrelated in sequence, the two B. pseudomallei nuclease domains share similar folds and active-site architectures. By contrast, the CdiIE479 and CdiI1026b immunity proteins share no significant sequence or structural homology. CdiA-CTE479 and CdiA-CT1026b are both tRNases; however, each nuclease cleaves tRNA at a distinct position. We used a molecular docking approach to model each toxin bound to tRNA substrate. The resulting models fit into electron density envelopes generated by small-angle x-ray scattering analysis of catalytically inactive toxin domains bound stably to tRNA. CdiA-CTE479 is the third CDI toxin found to have structural homology to the PD(D/E)XK superfamily. We propose that CDI systems exploit the inherent sequence variability and active-site plasticity of PD(D/E)XK nucleases to generate toxin diversity. These findings raise the possibility that many other uncharacterized CDI toxins may belong to the PD(D/E)XK superfamily.

Footnotes

  • ↵1 Supported in part by University of California at Irvine Bridge Funding.

  • ↵* This work was supported in part by National Institutes of Health Grants AI099687 and GM102318 (to C. W. G. and C. S. H.) and National Institutes of Health Project MINOS Grant GM105404. The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

  • The atomic coordinates and structure factors (code 5J4A) have been deposited in the Protein Data Bank (http://www.pdb.org/).

  • Received May 3, 2016.
  • Revision received July 18, 2016.
View this article with LENS
Table of Contents

This Article

  1. First Published on July 20, 2016 doi: 10.1074/jbc.M116.736074 The Journal of Biological Chemistry 291, 19387-19400.
  1. » Abstract(Free)
  2. Full Text(Free)
  3. PDF(Free)
  4. All Versions of this Article:
    1. M116.736074v1
    2. 291/37/19387 (most recent)

Article Usage Stats

  1. Article Usage Statistics

Submit your work to JBC.

You'll be in good company.