Unconventional Genomic Organization in the Alpha Subgroup of the Proteobacteria

Pulsed-field gel electrophoresis was used to analyze the genomic organization of 16 bacteria belonging or related to the family Rhizobiaceae of the alpha subgroup of the class Proteobacteria. The number and sizes of replicons were determined by separating nondigested DNA. Hybridization of an rrn gene probe was used to distinguish between chromosomes and plasmids. Members of the genus Agrobacterium all possess two chromosomes, and each biovar has a specific genome size. As previously demonstrated for Agrobacterium tumefaciens C58, the smaller chromosomes of Agrobacterium biovar 1 and Agrobacterium rubi strains appear to be linear. The genomes of Rhizobium strains were all of similar sizes but were seen to contain either one, two, or three megareplicons. Only one chromosome was present in the member of the related genus Phyllobacterium. We found one or two chromosomes in Rhodobacter and Brucella species, two chromosomes in Ochrobactrum anthropi, and one chromosome in Mycoplana dimorpha and Bartonella quintana; all of these genera are related to the Rhizobiaceae. The presence of multiple chromosomes is discussed from a phylogenetic and taxonomic point of view. Bacterial genomes were long considered to consist of a single circular chromosome. With the discovery of the existence of multiple circular chromosomes or a linear chromosome in some bacteria, this paradigm is no longer valid. Two different circular chromosomes were reported for Rhodobacter sphaeroides (39), Brucella melitensis 16M (27), and Leptospira interrogans (45), while three chromosomes are present in the genomes of Rhizobium meliloti (38), Burkholderia cepacia (7), and related species (33). A linear chromosome was reported first for the spirochete Borrelia burgdorferi (3, 11) and then for the gram-positive organisms Streptomyces lividans (25) and Rhodococcus fascians (8). We subsequently demonstrated that the genome of the gram-negative bacterium Agrobacterium tumefaciens C58 consisted of two chromosomes, one circular and the other linear (1). Most of the organisms presenting a multipartite genomic organization are confined to certain species within the purple bacteria (or Proteobacteriaceae), a phylum of the Bacteria, and perhaps this feature is correlated with the phylogeny of these bacteria. In the present study, we have investigated the genomic organization of organisms belonging to the alpha subgroup of the class Proteobacteria, particularly members of the genera Mycoplana, Ochrobactrum, Rhodobacter, Phyllobacterium, Rhizobium, and Agrobacterium. Although the first three genera do not belong to the family Rhizobiaceae, 16S rRNA sequence comparisons suggest that they belong to a tight phylogenetic group which also includes the genera Brucella and Bartonella (Rochalimaea) (9, 43). MATERIALS AND METHODS