Rhizobium meliloti exists either as a free-living soil organism or as a differentiated endosymbiont bacteroid form within the nodules of its host plant, alfalfa (Medicago sativa), where it fixes atmospheric N 2 . Differentiation is accompanied by major changes in DNA replication and cell division. In addition, R. meliloti harbors three unique large circular chromosome-like elements whose replication coordination may be complex. As part of a study of DNA replication control in R. meliloti, we isolated a dnaA homolog. The deduced open reading frame predicts a protein of 57 kDa that is 36% identical to the DnaA protein of Escherichia coli, and the predicted protein was confirmed by immunoblot analysis. In a comparison with the other known DnaA proteins, this protein showed the highest similarity to that of Caulobacter crescentus and was divergent in some domains that are highly conserved in other unrelated species. The dnaA genes of a diverse group of bacteria are adjacent to a common set of genes. Surprisingly, analysis of the DNA sequence flanking dnaA revealed none of these genes, except for an rpsT homolog, also found upstream of dnaA in C. crescentus. Instead, upstream of rpsT lie homologs of fpg, encoding a DNA glycosylase, and fadB1, encoding an enoyl-coenzyme A hydratase with a strikingly high (53 to 55%) level of predicted amino acid identity to two mammalian mitochondrial homologs. Downstream of dnaA, there are two open reading frames that are probably expressed but are not highly similar to any genes in the databases. These results show that R. meliloti dnaA is located within a novel gene arrangement.Rhizobium meliloti bacteria differentiate into symbiotic nitrogen-fixing bacteroids within the root nodules of alfalfa (13,26). This process, which converts growing free-living bacteria into intracellular forms, is accompanied by significant changes in cell physiology and metabolism (44,46). One of the more striking changes that occur is the cessation of DNA replication and cell division. To initiate our studies of genes involved in cell cycle regulation, we previously isolated two unique ftsZ genes, and we are now studying their roles in R. meliloti cell division (29). Since proper DNA replication is normally a prerequisite for cell septation, we are interested in identifying key DNA replication genes that may serve as control points. In addition, the tripartite genome of R. meliloti, which consists of a main chromosome and two large megaplasmids, is a unique model system for studying the coordination and segregation of multiple prokaryotic chromosomes. Thus, it is crucial to understand the functions of key replication genes in order to elucidate both normal DNA replication and segregation events in free-living R. meliloti cells and their alterations during differentiation.