SAM-AMP lyases in CRISPR defence and anti-defence

ABSTRACTType III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation of ancillary effectors. Although most signal via cyclic oligoadenylate (cOA), an alternative class of signalling molecule SAM-AMP, formed by conjugating ATP and S-adenosyl methionine, was described recently. SAM-AMP activates a trans-membrane effector of the CorA magnesium transporter family to provide anti-phage defence. Intriguingly, immunity also requires SAM-AMP degradation by means of a specialised CRISPR-encoded NrN family phosphodiesterase inBacteroides fragilis. InClostridium botulinum, thenrngene is replaced by a gene encoding a SAM-AMP lyase. Here, we investigate the structure and activity ofC. botulinumSAM-AMP lyase, which can substitute for thenrngene to provide CorA-mediated immunity inEscherichia coli. The structure of SAM-AMP lyase bound to its reaction product methylthioadenosine-AMP (MTA-AMP) reveals key details of substrate binding and turnover by this PII superfamily protein. Bioinformatic analyses reveal candidate phage-encoded SAM-AMP lyases and we demonstrate that one, hereafter named AcrIIIB4, degrades SAM-AMP efficientlyin vitro.