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. CDIand 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.

CdiA Effectors Use Modular Receptor-Binding Domains To Recognize Target Bacteria

“…To prevent self-intoxication, CDI + bacteria produce CdiI immunity proteins, which bind the CdiA-CT domain and neutralize its activity. Because CdiA-CT sequences are highly variable and the domains have distinct three-dimensional structures (16, 20–23), immunity proteins protect against only cognate toxins deployed by sibling cells. Thus, CDI confers a selective advantage against nonisogenic competitors, and toxin immunity polymorphism provides a mechanism for self/nonself discrimination.…”

Activation of contact-dependent antibacterial tRNase toxins by translation elongation factors

“…Burkholderia pseudomallei isolates K96243, 1026b, and E479 deploy tRNase toxins with distinct specificities. CdiA-CT K96243 has anticodon nuclease activity on tRNA His , tRNA Asp , tRNA Asn , and tRNA Tyr isoacceptors, and CdiA-CT E479 cleaves the T-loop of tRNA molecules between conserved residues Ψ54 and T55 (13,14). CdiA-CT II Bp1026b preferentially cleaves within the aminoacyl acceptor stem of tRNA Ala to block translation (15).…”

Are CDI Systems Multicolored, Facultative, Helping Greenbeards?

“…A VENN or Nx(E/Q)LYN motif delineates the conserved and variable regions. The variable CdiA-CT and BcpA-CT domains contain the toxic activity, with most being predicted, and some shown, to function as DNases or RNases (Box 1) [18–23]. When produced within, or delivered to, the cytoplasm of a susceptible bacterium, these toxins degrade DNA or specific tRNAs, resulting in growth inhibition or cell death (Figure 2C).…”

“…This functional variability results from structural differences, and from differences in toxin–immunity interactions. The interface at which a toxin and an immunity protein interact can be composed of electrostatic interactions, hydrogen-bonds, ionic bonds, and/or covalent bonds, and may cover 10–20% of the total surface area of the toxin or immunity domains [18,21,22]. In many cases, the complex formed by the toxin and immunity proteins has better thermal stability than either protein on its own [18,21].…”

“…The interface at which a toxin and an immunity protein interact can be composed of electrostatic interactions, hydrogen-bonds, ionic bonds, and/or covalent bonds, and may cover 10–20% of the total surface area of the toxin or immunity domains [18,21,22]. In many cases, the complex formed by the toxin and immunity proteins has better thermal stability than either protein on its own [18,21]. Regardless of toxin mechanism, immunity proteins may alter toxin activity by (i) blocking the active site of the toxin, or (ii) by binding elsewhere and, presumably, changing the structure and/or activity of the toxin.…”