A viral ADP-ribosyltransferase attaches RNA chains to host proteins

The mechanisms by which viruses hijack their host's genetic machinery are of current interest. When bacteriophage T4 infects Escherichia coli, three different ARTs (ADP-ribosyltransferases) reprogram the host's transcriptional and translational apparatus through ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as substrate. Recently, NAD was identified as a 5'-modification of cellular RNAs. Here, we report that T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as substrate and attaches entire RNA chains to acceptor proteins in an “RNAylation” reaction. ModB specifically RNAylates ribosomal proteins rS1 and rL2 at defined arginine residues, and selected E. coli and T4 phage RNAs are linked to rS1 in vivo. T4 phages that express an inactive mutant of ModB show a decreased burst size and slowed lysis of E. coli. Our findings reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer to proteins. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host's translation machinery. This work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections, RNAylation may have far-reaching implications. Overall design: Exponentially growing E. coli with endogenously His-tagged rS1 were infected with T4 phage WT or T4 phage ModB R73A,G74A or not infected for 8 minutes. His-tagged rS1 was captured and covalently bound RNA was reverse transcribed and sequenced using our RNAylomeSeq pipeline. His-tagged rS1 RNAylated with NAD-RNAI was used as a spike-in to monitor success of capture of RNAylated RNAs by RNAylomeSeq. Uninfected and ModB R73A,G74A infected samples serve as negative controls for the WT infected samples.