If every gene in the α-proteobacteria evolved by vertical descent, all genes would support the same tree topology. This is obviously not the case: only 33–97% of all genes have a most similar homologue that is also an α-proteobacterial species (Esser et al. 2007
). Furthermore, these genomes show a 10-fold variation in genome size, ranging from 1 to more than 9
Mbp (), with species-specific genes counting in the thousands (Boussau et al. 2004
). Thus, we may ask: are all genes equally flexible and how does this variability correlate with adaptations to specific growth niches?
Present in all species, including even the smallest genomes, are approximately 200 genes for DNA, RNA and protein syntheses and another 40 genes for nucleotide and cofactor biosyntheses (Boussau et al. 2004
). Gene content statistics for different functional categories show weak increases in gene number with genome size for genes involved in basic information processes
, such as transcription and translation (approx. 4 genes Mbp−1
; Boussau et al. 2004
). Much more dramatic increases are observed for genes involved in adaptability processes,
such as energy metabolism, transport and regulatory functions (approx. 80–100
), with some of the smallest genomes having virtually no regulatory genes (Boussau et al. 2004
We anticipate these variations in gene content to reflect the quality and stability of the growth environment. Indeed, by mapping the fluctuations in genome size onto the species tree, periods of massive genome reduction and expansion can be identified with hundreds of genes lost and gained in direct association with important environmental shifts (Boussau et al. 2004
). For example, bacteria adapted to the cytoplasm of eukaryotic host cells, which is a relatively static and rich growth environment, have evolved towards small genomes, whereas free-living bacteria adapted to soil, which is more variable in nutritional quality, have genomes of much larger sizes. Thousands of genes have been eliminated and thousands of genes have been acquired. Below, we discuss the mechanisms underlying these dramatic changes in gene content.