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Large extrachromosomal replicons in many members of theα-proteobacteria encode genes that are required for plant or animal pathogenesis or symbiosis. Most of these replicons encoderepABCgenes that control their replication and faithful segregation during cell division. In addition to its chromosome, the plant endosymbiontSinorhizobium melilotialso maintains the 1.4 Mb pSymA and 1.7 Mb pSymB symbiotic megaplasmids both of which arerepABC-type replicons. In allrepABCloci that have been characterized, an apparently untranslated intergenic region between therepBandrepCgenes encodes a strong incompatibility determinant (referred to as incα). Here we report the isolation of mutations within the incα regions of pSymA and pSymB that eliminate incompatibility. These mutations map to and inactivate a promoter in the intergenic region that drives the expression of an approximately 56 nucleotide untranslated RNA molecule that mediates incompatibility. This gene, that we have namedincA, is transcribed antisense to therepABCgenes. Our analysis suggests that theincAgene is conserved inrepABCloci from a diverse spectrum of bacteria. [ABSTRACT FROM AUTHOR]