Unconventional genomic organization in the alpha subgroup of the Proteobacteria

Abstract

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.

FIG. 1

PFGE of intact DNAs of bacterial species belonging to the family Rhizobiaceae: separation of large replicons. Lanes: 1, Saccharomyces pombe; 2, A. vitis CFBP 2721; 3, A. vitis CFBP 2607; 4, A. tumefaciens C58; 5, A. tumefaciens ATCC 23308^T; 6, A. radiobacter CFBP 2414^T; 7, A. rhizogenes ATCC 11325^T; 8, A. rhizogenes K84; 9, A. rubi ATCC 13335^T; 10, Rhizobium fredii ATCC 35423^T; 11, Rhizobium leguminosarum bv. phaseoli ATCC 14482^T; 12, Rhizobium leguminosarum bv. trifolii ATCC 14480^T; far right, H. wingei. The positions of molecular size markers are indicated on both sides of the gel.

FIG. 2

Hybridization of large replicons with the 16S rRNA probe. (Upper panel) 1, A. radiobacter CFBP 2414^T; 2, A. rhizogenes K84; 3, A. tumefaciens C58; 4, A. rhizogenes ATCC 11325^T; 5, A. rubi ATCC 13335^T; 6, Rhizobium fredii ATCC 35423^T; 7, Rhizobium leguminosarum bv. trifolii ATCC 14480^T; 8, Rhizobium meliloti 2011. (Lower panel) Lanes: 1, O. anthropi ATCC 49188^T; 2, P. myrsinacearum ATCC 43590^T; 3, Rhodobacter capsulatus ATCC 11166; 4, Rhizobium meliloti 2011; 5, A. tumefaciens C58. The positions of molecular size markers are shown on both sides of the two panels.

FIG. 3

PFGE of intact DNAs of bacterial species belonging to the family Rhizobiaceae: separation of small replicons. Lanes: 1, Saccharomyces cerevisiae; 2, A. rhizogenes K84; 3, A. vitis CFBP 2721; 4, A. vitis CFBP 2607; 5, A. tumefaciens C58; 6, H. wingei; 7, A. tumefaciens ATCC 23308^T; 8, A. radiobacter CFBP 2414^T; 9, A. rubi ATCC 13335^T; 10, Rhizobium meliloti 2011; 11, Rhizobium fredii ATCC 35423^T; 12, Rhizobium leguminosarum bv. phaseoli ATCC 14482^T; 13, R. leguminosarum bv. trifolii ATCC 14480^T; 14, Saccharomyces cerevisiae. The positions of molecular size markers are shown on both sides of the gel.

FIG. 4

PFGE of intact DNAs of bacterial species related to the Rhizobiaceae: separation of large replicons. Lanes: 1, Schizosaccharomyces pombe; 2, Rhodobacter capsulatus ATCC 11166; 3, P. myrsinacearum ATCC 43590^T; 4, O. anthropi ATCC 49188^T; 5, O. anthropi LMG 3301; 6, M. dimorpha ATCC 4279^T; 7, Rhizobium meliloti 2011; 8, A. tumefaciens C58; 9, H. wingei. The positions of molecular size markers are shown on both sides of the gel.

FIG. 5

PFGE of intact DNAs of bacterial species related to the Rhizobiaceae: separation of small replicons. Lanes: 1, lambda DNA ladder; 2, H. wingei; 3, P. myrsinacearum ATCC 43590^T; 4, M. dimorpha ATCC 4279^T; 5, Rhodobacter capsulatus ATCC 11166; 6, H. wingei; 7, O. anthropi ATCC 49188^T; 8, O. anthropi LMG 3301; 9, Saccharomyces cerevisiae; 10, lambda DNA ladder. The positions of molecular size markers are indicated to the left and right.

FIG. 6

Phylogenetic tree showing the genomic organization of organisms belonging to the α2 subgroup of the Proteobacteria (plus Rhodobacter species, which belong to the α3 subgroup) (redrawn from reference 43). Organisms with complex genomes are indicated in boldface and underlined.