Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella Reference Collection B (SARB) and SARC sets

Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are clea ved after transcription and lead to the presence of fragmented rRNA,which i s incorporated into the ribosomes without religation but is nevertheless fu nctional. The fragmentation of rRNA and the number of IVSs in all 72 strain s of the Salmonella Reference Collection B set and 16 strains of the Salmon ella Reference Collection C set, which have been established on the basis o f multilocus enzyme electrophoresis (MLEE), were analyzed in the present st udy. Fragmentation of 23S rRNA was restricted to conserved cleavage sites l ocated at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs ha ve been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for ma intenance of RNase III cleavage sites. The distribution of the number of IV Ss carried by the different strains in the seven rrl genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern amon g the various Salmonella strains tested; this indicates that the IVSs are f requently exchanged between strains by lateral transfer. All eight subspeci es of the genus Salmonella, including subspecies V represented by Salmonell a bongori, have IVSs in both helix 25 and helix 45; this indicates that IVS s entered the genus after its divergence from Escherichia coli (more than 1 00 million years ago) but before separation of the genus Salmonella into ma ny forms or that they were in the ancestor but have been lost from Escheric hia.