The structure of a contact-dependent growth-inhibition (CDI) immunity protein fromNeisseria meningitidisMC58

Abstract

Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI + bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein from Neisseria meningitidis MC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of RNA-binding proteins, but appears to lack the characteristic nucleic acid-binding motif of this family. Sequence homology suggests that the cognate CdiA-CT is related to the eukaryotic EndoU family of RNA-processing enzymes. A homology model is presented of the CdiA-CT based on the structure of the XendoU nuclease from Xenopus laevis. Molecular-docking simulations predict that the CdiA-CT toxin active site is occluded upon binding to the CdiI immunity protein. Together, these observations suggest that the immunity protein neutralizes toxin activity by preventing access to RNA substrates.

Contact-Dependent Growth Inhibition (CDI) and CdiB/CdiA Two-Partner Secretion Proteins

“…CdiI ECL is structurally similar to the Whirly family of single-stranded DNA binding proteins 26; 47 , but was recently proposed to have evolved from an ancestral SUKH family immunity protein 38; 48 . Intriguingly, the CdiI o2 MC58-1 immunity protein encoded by locus NMB0503 of Neisseria meningiditis MC58 also shares some structural homology with Whirly proteins 49 . The cognate toxin for this latter immunity protein is a predicted EndoU RNase 37; 49 .…”

“…Intriguingly, the CdiI o2 MC58-1 immunity protein encoded by locus NMB0503 of Neisseria meningiditis MC58 also shares some structural homology with Whirly proteins 49 . The cognate toxin for this latter immunity protein is a predicted EndoU RNase 37; 49 . Because EndoU and BECR toxin folds are related 37 , it appears that the Ntox21 and EndoU nuclease families evolved from a common ancestor that was associated with an SUKH immunity protein.…”

Functional plasticity of antibacterial EndoU toxins

“…A DALI server search for structural homologs of CdiI STECO31 returned NMB0503 from N. meningitidis MC58 (PDB ID:4Q7O, (Tan et al, )) with Z = 13.4 and rmsd 2.6 Å over 111 Cα atoms (Fig. A).…”

Contact-Dependent Growth Inhibition in Bacteria: Do Not Get Too Close!

“…This type of species competition has been discovered in several Gram-negative microorganisms including E. coli [28,30,32,[35][36][37][38][40][41][42][43][44][47][48][49][50][51], Burkholderia spp. (Burkholderia thailandensis, Burkholderia dolosa) [52][53][54][55][56][57][58][59], N. meningitidis [60], P. aeruginosa [61][62][63][64], and Acinetobacter spp. (A. baumannii, Acinetobacter baylyi) [65][66][67][68] (Table 1), while proteins similar to CdiA-CT toxin were identified also in Gram-positive species including Bacillus, Listeria, Clostridium, and Streptococcus [31].…”

“…The crystal structure of the CdiI immunity protein. [60] Enterobacter cloacae CdiA-CT ECL /immunity protein complex. [70] Xenorhabdus doucetiae…”