A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti.

Abstract

Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large reverse transcriptase (RT)-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with podovirus-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.IMPORTANCEIn this study, we report the functional characterization of a UG5-large reverse transcriptase-associated defense system (DRT11) encoded on the pSymA megaplasmid of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Using a combination of phylogenetic, metagenomic, genomic, and experimental approaches, we demonstrate that DRT11 functions as a bona fide antiviral defense module, providing protection against naturally occurring rhizosphere phages through a minimal reverse transcriptase-nitrilase architecture. This work establishes direct functional evidence for antiviral activity within the UG5 family and clarifies the evolutionary placement of UG5-associated systems within the broader UG radiation.