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

• DOI: 10.1074/jbc.m116.736074
• Publication Date: 2016-07-22T00:07:44Z
• Authors: Parker M. Johnson; Grant C. Gucinski; Fernando Garza-Sá...; Timothy Wong; Li-Wei Hung; Christopher S. Hayes; Celia W. Goulding
• Keywords: 570; Protein Structure; crystal structure; Biochemistry & Molecular Biology; Biomedical and clinical sciences; Burkholderia pseudomallei; 610; Medical and Health Sciences; Quaternary; 03 medical and health sciences; small-angle x-ray scattering; Bacterial Proteins; Protein Domains; RNA, Transfer; Biodefense; Endoribonucleases; Minority Health; toxin; Protein Structure, Quaternary; 0303 health sciences; protein complex; Bacterial; Membrane Proteins; Biological Sciences; immunity complexes; 3. Good health; Transfer; Molecular Docking Simulation; Biological sciences; RNA, Bacterial; Emerging Infectious Diseases; Infectious Diseases; Chemical sciences; toxin/immunity complexes; Multiprotein Complexes; Chemical Sciences; RNA; Biochemistry and Cell Biology; ribonuclease; tRNase

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/CdiI(E479) toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CT(E479) 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-CT(E479) 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 CdiI(E479) and CdiI(1026b) immunity proteins share no significant sequence or structural homology. CdiA-CT(E479) and CdiA-CT(1026b) 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-CT(E479) 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.