Sequence and copy number of the Xanthomonas campestris pv. campestris gene encoding 16S rRNA

A 6.7-kb Sau3A1 fragment containing ribosomal RNA genes was cloned from the chromosome of Xanthomonas campestris pv. campestris strain 17 by a PCR-based strategy. Nucleotide sequence was determined for the 16S rRNA gene (1,544 nt). This gene has a G+C content of 54.9% which is similar to the 16S rRNA genes of Escherichia coli and Pseudomonas aeruginosa but different from the value reported for the whole X. campestris chromosome (64%). Sequence alignment revealed that AGGAGG is consensus for ribosome binding, with the internal GGAG to be paired most frequently with the anti-Shine-Dalgarno sequence. This consensus sequence was found in the regions upstream from the initiation codon of 98 Xanthomonas genes among 116 aligned, but not in the remaining genes. This suggests that about 16% of the Xanthomonas genes do not possess typical ribosome binding sites and another mechanism may be required for recognition of correct translation initiation sites. Two rrn operons were detected in Xc17 chromosome by pulsed-field gel electrophoresis and Southern hybridization.