We are nearing completion of the complete 760 Kbp genomic sequence of the bacterium Ureaplasma urealyticum serovar 3 (Uu). In addition to annotating this sequence, we have compared features of the ribosomal protein gene cluster of the Uu sequence with that of the related bacterium, Mycoplasma genitalium (Mg - 580 Kbp), Mycoplasma pneumoniae (Mp - 816 Kbp) Mycoplasma capricolum (~1.1 Mbp), as well as to the published sequences for Bacillus subtilis (Bs - ~4.2 Mbp), Haemophilus influenzae (Hi - 1.8 Mbp) and Escherichia coli (Ec - 4.6 Mbp). This gene cluster begins with ribosomal protein S10, and ends with ribosomal protein L17, and contains 24-26 ribosomal genes with a few other gene inserts. Exact synteny is maintained between the four Mycoplasma species, while gene order with Ec and Hi is maintained with the exception of the insertion/deletion of ribosomal proteins L30, S4, and a few other protein coding genes of unrelated function. This cluster is comprised of three separate regulatory operons: S10, spc, and alpha. The gene order for Bs is a hybrid between the Mycoplasma species and that for Ec and Hi. In general, the Uu proteins are most similar to the other Mycoplasma species, averaging 68% similarity and 57% identity throughout this gene cluster. Uu ribosomal proteins average 64% similarity and 53% identity with Bs, Hi and Ec ribosomal proteins within this same region. Mg and Mp proteins show 87/80 % similarity/identity between each other within this region.
Comparisons of the lengths of the intergenic regions between coding sequences within this gene cluster show that Mg and Mp maintain very small intergenic distances of only a few nucleotides on average, while Uu, Mc, Bs, Hi, and Ec all have intergenic region lengths averaging 20 or more nucleotides. Genome size alone cannot be directing the evolution of intergenic region length, since the Uu genome is equivalent in size to the Mp genome, and much smaller than the Ec genome, but maintains an intergenic region length much closer to the latter organism.