Nucleotide sequence analysis of the 23S ribosomal RNA-encoding gene of Bartonella bacilliformis

We report the cloning and characterization of the 23S ribosomal RNA (rRNA)-encoding gene (rDNA) of Bartonella bacilliformis (Bb). The 2821-bp gene is preceded by an 11-nucleotide (nt) inverted repeat (IR) located 81 nt upstream in the tRNA(Ala)-23S rDNA intergenic spacer. The gene is followed by an 8-nt IR, five nt downstream in the 23S-5S rDNA intergenic spacer. The nt sequence of the Bb 23S rDNA is most similar to the 23S rDNA of Rhodopseudomonas palustris (Rp), with 85.4% sequence identity. The Bb 23S rDNA has 77.8% identity to the same gene from Escherichia coli (Ec). Secondary structure predictions indicate that the large subunit (LSU) Bb rRNA contains two smaller stem-loops at nt 1459-1544 and 1658-1685, as compared to the corresponding loops from Ec (nt 1405-1597 and 1707-1751, respectively). In addition, the Bb 23S rRNA has a large 72-nt stem-loop at nt 130-201, as compared to the Ec 18-nt stem-loop (nt 131-148). There is no Bb homologue of the 15-nt stem-loop at the 3' end of the Ec molecule (nt 2791-2805). The Bb 23S rRNA lacks the large stem-loop present in the LSU rRNA of closely related Rhodobacter sphaeroides (Rs) (nt position 1225-1331) which is thought to be involved in cleavage of 23S RNA precursor molecules into 16S and 14S rRNA species. This is the first LSU rDNA nt sequence for any member of the Bartonellaceae family.