Evolutionary dynamics of proteinaceous MAMPs reveals intrabacterial antagonism of plant immune perception

Plants and animals detect biomolecules termed Microbe-Associated Molecular Patterns (MAMPs) and induce immune responses. The impact of diverse multi-copy MAMPs on immune induction is unknown. We characterized the evolutionary trajectories of five proteinaceous MAMPs and the effect of copy number and sequence variation on plant immune outcomes. From 4,228 plant-associated bacterial genomes, 34,262 MAMPs were identified. Natural variation was constricted, enabling characterization of immune perception across thousands of bacteria. We characterized the immunogenic outcomes of two MAMPs with different evolutionary trajectories the Elongation Factor Tu (EF-Tu) epitope elf18 and Cold Shock Protein (CSP) epitope csp22. EF-Tu is a single-copy gene and 90% of elf18 epitopes are immunogenic. Conversely, CSPs are multi-copy with 99.8% of bacteria carrying at least one immunogenic CSP and only 54% of csp22 epitopes are immunogenic. We uncovered a new mechanism for immune evasion, intrabacterial antagonism, from a non-immunogenic actinobacterial CSP that blocks perception of immunogenic forms.