Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Abstract

Animal intracellular Proteobacteria of the alpha subclass without plasmids and containing one or more chromosomes are phylogenetically entwined with opportunistic, plant-associated, chemoautotrophic and photosynthetic alpha Proteobacteria possessing one or more chromosomes and plasmids. Local variations in open environments, such as soil, water, manure, gut systems and the external surfaces of plants and animals, may have selected alpha Proteobacteria with extensive metabolic alternatives, broad genetic diversity, and more flexible and larger genomes with ability for horizontal gene flux. On the contrary, the constant and isolated animal cellular milieu selected heterotrophic alpha Proteobacteria with smaller genomes without plasmids and reduced genetic diversity as compared to their plant-associated and phototrophic relatives. The characteristics and genome sizes in the extant species suggest that a second chromosome could have evolved from megaplasmids which acquired housekeeping genes. Consequently, the genomes of the animal cell-associated Proteobacteria evolved through reductions of the larger genomes of chemoautotrophic ancestors and became rich in adenosine and thymidine, as compared to the genomes of their ancestors. Genome organisation and phylogenetic ancestor-descendent relationships between extant bacteria of closely related genera and within the same monophyletic genus and species suggest that some strains have undergone transition from two chromosomes to a single replicon. It is proposed that as long as the essential information is correctly expressed, the presence of one or more chromosomes within the same genus or species is the result of contingency. Genetic drift in clonal bacteria, such as animal cell-associated alpha Proteobacteria, would depend almost exclusively on mutation and internal genetic rearrangement processes. Alternatively, genomic variations in reticulate bacteria, such as many intestinal and plant cell-associated Proteobacteria, will depend not only on these processes, but also on their genetic interactions with other bacterial strains. Common pathogenic domains necessary for the invasion and survival in association with cells have been preserved in the chromosomes of the animal and plant-associated alpha Proteobacteria. These pathogenic domains have been maintained by vertical inherence, extensively ameliorated to match the chromosome G + C content and evolved within chromosomes of alpha Proteobacteria.

Genome Structure of the GenusAzospirillum

“…All five species analyzed showed multiple replicons, and the presence of 16S rDNA genes in several of them supports the suggestion that the Azospirillum genome is split into several chromosome-like structures. In A. brasilense and A. lipoferum, these structures were found in either linear or circular DNA, as has also been observed for other species within the alpha subclass of the Proteobacteria (17).…”

Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

“…The small genomes and isolated lifestyles of obligate intracellular bacteria are thought to reduce the opportunities for gene acquisition. It has also been hypothesized that genetic exchanges are minored in these species because their relatively constant intracellular environment does not select for the genetic diversity promoted by more challenging environments (Moreno 1998). These early views are now progressively changing with the accumulation of genomic data, which provide evidence for a better appraisal of the nature and extent of genetic exchange in intracellular bacteria (Bordenstein and Reznikoff 2005).…”

Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies

“…The relation between host-restricted life style and a small genome size is patent in bacteria, particularly in alpha Proteobacteria (33). O. intermedium is a free-living bacterium and has a larger genome than its phylogenetic neighbors with an intracellular life style, such as Brucella and Bartonella (17,33).…”

“…O. intermedium is a free-living bacterium and has a larger genome than its phylogenetic neighbors with an intracellular life style, such as Brucella and Bartonella (17,33). It might be suggested that the 1-year restriction of isolates ADV1 to -7 to a very narrow ecological niche, i.e., the human respiratory system, led to reductive evolution (2,33).…”