Whole-genome analyses of speciation events in pathogenic Brucellae

Abstract

Despite their high DNA identity and a proposal to group classical Brucella species as biovars of Brucella melitensis, the commonly recognized Brucella species can be distinguished by distinct biochemical and fatty acid characters, as well as by a marked host range (e.g., Brucella suis for swine, B. melitensis for sheep and goats, and Brucella abortus for cattle). Here we present the genome of B. abortus 2308, the virulent prototype biovar 1 strain, and its comparison to the two other human pathogenic Brucella species and to B. abortus field isolate 9-941. The global distribution of pseudogenes, deletions, and insertions supports previous indications that B. abortus and B. melitensis share a common ancestor that diverged from B. suis. With the exception of a dozen genes, the genetic complements of both B. abortus strains are identical, whereas the three species differ in gene content and pseudogenes. The pattern of species-specific gene inactivations affecting transcriptional regulators and outer membrane proteins suggests that these inactivations may play an important role in the establishment of host specificity and may have been a primary driver of speciation in the genus Brucella. Despite being nonmotile, the brucellae contain flagellum gene clusters and display species-specific flagellar gene inactivations, which lead to the putative generation of different versions of flagellum-derived structures and may contribute to differences in host specificity and virulence. Metabolic changes such as the lack of complete metabolic pathways for the synthesis of numerous compounds (e.g., glycogen, biotin, NAD, and choline) are consistent with adaptation of brucellae to an intracellular life-style.

FIG. 1.

Whole-genome comparison of B. abortus 2308, B. melitensis 16M, and B. suis 1330. A linear representation of both chromosomes displays the approximate locations and sizes (in kilobases, below features) of major insertions, deletions, and repetitive elements (including IS711 and rRNA sequences, as well as repeated phage and IS3 family elements). Also indicated are the approximate locations and sizes (in kilobases, above features) of inversions found within the chromosomes of the three Brucella spp. The hashed boxes indicate regions that were found to be missing from B. abortus strain 2308 but were present in strain 9-941s. Note that the large inversion in ChrII of B. abortus has been flipped in this diagram for better visual alignment (of the features within this inversion) with the other genomes. Refer to the inset for definitions of genome features.

FIG. 2.

Venn diagram displaying the distribution of pseudogenes among the Brucella genomes. The total number of pseudogenes in each section is shown in blue; distribution by chromosome is indicated (ChrI/ChrII). The total number of pseudogenes within each species genome is shown outside the circles and under the species names. Note that these numbers do not reflect genes that are absent from the genomes.

FIG. 3.

Distribution of pseudogenes by functional category. Functional classifications are as follows: J, translation ribosomal structure and biogenesis; K, transcription; L, DNA replication, recombination, and repair; D, cell division; V, defense mechanisms; T, signal transduction; M, cell envelope, biogenesis, and outer membrane; N, cell motility and secretion; U, intracellular traffic, secretion, and vesicular transport; O, posttranslational modification, protein turnover, and chaperons; C, energy production and conversion; G, carbohydrate metabolism; E, amino acid metabolism; F, nucleotide metabolism; H, coenzyme metabolism; I, lipid metabolism; Q, secondary metabolite biosynthesis and catabolism; R, general function prediction only; S, function unknown; X, no cluster of orthologous groups (COG); TR, transport.