CdiA from Enterobacter cloacae Delivers a Toxic Ribosomal RNase into Target Bacteria

Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. CDI+ cells export large CdiA effector proteins, which carry a variety of C-terminal toxin domains (CdiA-CT). CdiA-CT toxins are specifically neutralized by cognate CdiI immunity proteins to protect toxin-producing cells from autoinhibition. Here, we use structure determination to elucidate the activity of a CDI toxin from Enterobacter cloacae (ECL). The structure of CdiA-CTECL resembles the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis. In accord with this structural homology, we show that CdiA-CTECL uses the same nuclease activity to inhibit bacterial growth. Surprisingly, although colicin E3 and CdiAECL carry equivalent toxin domains, the corresponding immunity proteins are unrelated in sequence, structure, and toxin-binding site. Together, these findings reveal unexpected diversity among 16S rRNases and suggest that these nucleases are robust and versatile payloads for a variety of toxin-delivery platforms. [Display omitted] •Contact-dependent growth inhibition (CDI) systems mediate inter-bacterial competition•We present the structure of the Enterobacter cloacae CDIECL toxin/immunity complex•The CDIECL toxin displays a similar fold and nuclease activity as colicin E3•The structural similarities between these toxins likely reflect convergent evolution Contact-dependent growth inhibition (CDI) systems deliver toxins to mediate interbacterial competition. Beck et al. show that the CDI toxin from Enterobacter cloacae cleaves 16S rRNA to inhibit cell growth. Because it is not related to known ribosomal RNases, CDI toxin reveals unexpected diversity in these enzymes.