Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RNA-Seq)
Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. During infection, newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA, with consequent liberation of the toxin CmdT, an ADP-ribosyltransferase. Strikingly, CmdT does not target a protein, DNA, or structured RNA, the known targets of other ADP-ribosyltransferases. Instead, CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs to robustly block mRNA translation and viral replication. Our work reveals both a new mechanism of anti-phage defense and a new class of ADP-ribosyltransferases that targets mRNA. Overall design: The goal of this experiment is to look globally at the changes in T4 transcription +/- cmdTAC expression. RNA was harvest from T4 infected cells +/- cmdTAC at 15 and 30 minutes post-infection. Harvested RNA was rRNA depleted and made into a cDNA library for sequencing on an Illumina NextSeq 5000 machine. We then calculated the transcripts per million (TPM) values for all coding sequences in the T4 genome at both timepoints post-infection and compared the TPM values between +cmdTAC and -cmdTAC samples, looking at changes in the TPM ratio between timepoints and for T4 genes of different peak expression times.