GNAT toxins of bacterial toxin–antitoxin systems: acetylation of charged tRNAs to inhibit translation

Abstract

GCN5-related N-acetyltransferase (GNAT) is a huge superfamily of proteins spanning the prokaryotic and eukaryotic domains of life. GNAT proteins usually transfer an acetyl group from acetyl-CoA to a wide variety of substrates ranging from aminoglycoside antibiotics to large macromolecules. Type II toxin-antitoxin (TA) modules are typically bicistronic and widespread in bacterial and archael genomes with diverse cellular functions. Recently, a novel family of type II TA toxins was described, which presents a GNAT-fold and functions by acetylating charged tRNA thereby precluding translation. These GNAT toxins are usually associated with a corresponding ribbon-helix-helix-fold (RHH) antitoxin. In this issue, Qian et al. describes a unique GNAT-RHH TA system, designated KacAT, from a multidrug resistant strain of the pathogen, Klebsiella pneumoniae. As most type II TA loci, kacAT is transcriptionally autoregulated with the KacAT complex binding to the operator site via the N-terminus region of KacA to repress kacAT transcription. The crystal structure of the KacT toxin is also presented giving a structural basis for KacT toxicity. These findings expand our knowledge on this newly discovered family of TA toxins and the potential role that they may play in antibiotic tolerance and persistence of bacterial pathogens.

Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway

“…A major class of EVE proteins which formed a distinct cluster in our CLANS analysis (purple in Figure 2), is a fusion of EVE to the C-terminus of a GNAT-like acetyltransferase, often with a PIN RNase domain at the N-terminus ( Figure 7). GNAT and PIN domains both frequently function as toxins (Makarova, Wolf, and Koonin 2009;Matelska, Steczkiewicz, and Ginalski 2017;Yeo 2018). This variety of EVE proteins has been described previously in some detail by Iyer et al, who proposed that these proteins acetylate a DNA base, although the frequent presence of a PIN domain suggests that these systems employ RNA as a target or guide (Iyer et al 2013).…”

“…The PIN domain RNases function as toxins in a broad variety of bacterial, and especially, archaeal TA systems (Matelska, Steczkiewicz, and Ginalski 2017;Makarova, Wolf, and Koonin 2009). The GNAT domains also typically function as toxins (Yeo 2018), and HTH domain-containing antitoxins have been described as well (Chan, Espinosa, and Yeo 2016). The mechanistic details of these (PIN)-GNAT-EVE protein activities await experimental investigation, but some functional hints emerged from our analysis.…”

“…In light of the observations described above concerning (PIN)-GNAT-EVE proteins, targeting GNAT to modified DNA or RNA via EVE, conceivably, protects phages against host RM systems, perhaps, via toxicity to the host, whereas the addition of PIN is associated with host defense and likely counteracts the effect of GNAT-EVE. The GNAT-EVE proteins potentially target aminoacyl-tRNAs (aa-tRNAs) that harbor modifications recognized by EVE, given that GNAT toxins have been reported to acetylate aa-tRNAs (Wilcox et al 2018;Yeo 2018). Under this scenario, PIN-GNAT-EVE proteins would likely degrade toxic, acetylated aa-tRNAs generated by GNAT-EVE.…”

Bioinformatics and Functional Assessment of Toxin-Antitoxin Systems in Staphylococcus aureus

“…We screened for TA genes and predicted a total of 67 putative TA systems with Rasta bacteria, TADB, and PSI-BLAST. To make the classification more accurate, we used the TA systems of E. coli [ 4 ], Klebsiella pneumoniae [ 18 ], and Mycobacterium [ 5 , 19 ] as modal and manually curated each TA system and classified them into different families. We found type I, II, III, IV, and type V TA systems in S. aureus on the basis of software prediction, conserved domain analysis, and orthologues searches from Kyoto Encyclopedia of Genes and Genomes (KEGG).…”

“…The GNATs-like TA system is the new addition of the TA family that can prevent peptide bond formation by acetylating tRNA and inhibiting translation in Salmonella and Klebsilla [ 18 , 29 ]. The TacT toxin inhibits translation via acetylating the initiator tRNA, and induces persister cell formation [ 29 ].…”