Sequences around the fragmentation sites of the large subunit ribosomal RNA in the family Rhizobiaceae

We demonstrated that the representatives of the family Rhizobiaceae possess, instead of one single 23S rRNA molecule, three different sets of 23S-like rRNA fragments with sizes of about: 135 b and 2.6 kb (set 1); 135 b, 400 b, and 2.2 kb (set 2); 135 b and two molecules of about 1.3 kb (set 3). In two of the fragmentations, intervening sequences - IVS I and IVS II - are involved. The IVS I is connected to a cleavage of the 23S rRNA primary transcript into two molecules (135 b and 2.6 kb large). The IVS II is located at position 543 of the gene, and it leads to an additional processing of the 2.6 kb rRNA species into two molecules with sizes of about 400 b and 2.2 kb. In contrast to the IVS I, which is a common feature of all rhizobia, the IVS II is present in a limited number of strains only. The primary and secondary structures of the regions of the unmatured 23S rRNA transcript possessing IVS I (helix 9) and IVS II (helix 25) were analysed. On the basis of our analyses we propose secondary structure models of the parts of the matured 23S rRNA-like molecules of rhizobia corresponding to the helices 9 and 25. The third fragmentation of the rhizobial 23S rRNA represents a break in the central part of the 2.6 kb-large rRNA and it leads to an occurence of two fragments with approximately equal size of about 1.3 kb. We have demonstrated that the central fragmentation is not connected to the presence of IVSs but probably to a minor change in the nucleotide sequence in the central part of the 2.6 rRNA.