title: Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei.
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/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.
authors.affiliation: From the Departments of Molecular Biology and Biochemistry and.
authors.forename: Parker M
authors.initials: PM
authors.lastname: Johnson
authors.affiliation: the Biomolecular Science and Engineering Program and.
authors.forename: Grant C
authors.initials: GC
authors.lastname: Gucinski
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and.
authors.forename: Fernando
authors.initials: F
authors.lastname: Garza-Sánchez
authors.affiliation: From the Departments of Molecular Biology and Biochemistry and.
authors.forename: Timothy
authors.initials: T
authors.lastname: Wong
authors.affiliation: the Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545.
authors.forename: Li-Wei
authors.initials: LW
authors.lastname: Hung
authors.affiliation: the Biomolecular Science and Engineering Program and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and chayes@lifesci.ucsb.edu.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Hayes
authors.affiliation: From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California at Irvine, Irvine, California 92697, celia.goulding@uci.edu.
authors.forename: Celia W
authors.initials: CW
authors.lastname: Goulding
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016957:Burkholderia pseudomallei / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004722:Endoribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D062105:Molecular Docking Simulation; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000072417:Protein Domains; D020836:Protein Structure, Quaternary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D046912:Multiprotein Complexes; D012329:RNA, Bacterial; D012343:RNA, Transfer; D004722:Endoribonucleases
keywords: Burkholderia pseudomallei; crystal structure; protein complex; ribonuclease; small-angle x-ray scattering (SAXS); tRNase; toxin; toxin/immunity complexes