A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria

Abstract

Summary paragraphBacteria have developed mechanisms to communicate and compete with one another in diverse environments 1. A new form of intercellular communication, contact-dependent growth inhibition (CDI), was discovered recently in Escherichia coli 2. CDI is mediated by the CdiB/CdiA two-partner secretion system. CdiB facilitates secretion of the CdiA ‘exoprotein’ onto the cell surface. An additional immunity protein (CdiI) protects CDI+ cells from autoinhibition 2, 3. The mechanisms by which CDI blocks cell growth and CdiI counteracts this growth arrest are unknown. Moreover, the existence of CDI activity in other bacteria has not been explored. Here we show that the CDI growth inhibitory activity resides within the carboxy-terminal region of CdiA (CdiA-CT), and that CdiI binds and inactivates cognate CdiA-CT, but not heterologous CdiA-CT. Bioinformatic and experimental analyses show that multiple bacterial species encode functional CDI systems with high sequence variability in the CdiA-CT and CdiI coding regions. CdiA-CT heterogeneity implies that a range of toxic activities are utilized during CDI. Indeed, CdiA-CTs from uropathogenic E. coli and the plant pathogen Dickeya dadantii have different nuclease activities, each providing a distinct mechanism of growth inhibition. Finally, we show that bacteria lacking the CdiA-CT and CdiI coding regions are unable to compete with isogenic wild-type CDI+ cells in both laboratory media and upon a eukaryotic host. Taken together, these results suggest that CDI systems constitute an intricate immunity network that plays an important role in bacterial competition.

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

“…Contactdependent growth inhibition (CDI) represents one important form of interbacterial competition that is common among Gramnegative pathogens (1)(2)(3). CDI is mediated by the CdiB/CdiA family of two-partner secretion proteins, which assemble as a complex on the surface of CDI + bacteria.…”

“…Upon binding receptor, CdiA transfers its C-terminal toxin domain (CdiA-CT) into the target bacterium through an incompletely understood translocation mechanism (4,5). Genome and protein database surveys show that CdiA effectors carry a wide variety of distinct toxins (1,(6)(7)(8). CDI + cells protect themselves from self-intoxication by producing CdiI immunity proteins, which bind specifically to cognate CdiA-CT domains and neutralize their toxic activities.…”

“…Many other CdiA-CT toxins are nucleases that must be delivered into the target-cell cytoplasm to inhibit growth. CdiA-CT 3937 from Dickeya dadantii 3937 has potent DNase activity that destroys the target-cell chromosome (1,11), whereas the CdiA-CT ECL toxin from Enterobacter cloacae ATCC 13047 cleaves 16S rRNA to block protein synthesis (12). tRNA molecules are particularly common substrates for CDI nuclease toxins.…”

Unraveling the essential role of CysK in CDI toxin activation

“…The CdiA-CT EC536 region is composed of two domains that have distinct functions during CDI (9). The extreme C-terminal domain is an Ntox28 RNase family member (Pfam: PF15605) and is responsible for growth-inhibition activity (3,8). The N-terminal domain facilitates translocation of the tethered nuclease into the cytosol of target bacteria (9).…”

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

“…This operon organization and domain architecture indicates that these ARTs are toxins belonging to a recently described class of polymorphic toxins primarily implicated in intraspecific competition in bacteria, in which the C-terminal toxin domain is delivered into rival target cells. 32,70,77 Thus, in this case the ARG is an immunity protein that protects the producing cell against its own ART toxin. Thus, the use of genomically linked opposing ART and ARG pairs appears to be widespread in bacteria across a thematically diverse group of systems.…”