Fragmentations of the large-subunit rRNA in the family Rhizobiaceae

Abstract

A 130-nucleotide-long rRNA species corresponding to the 5 end of the 23S rRNA gene was found in 96 strains belonging to different Rhizobium, Bradyrhizobium, and Agrobacterium species. Additional fragmentation in the central region of the large-subunit rRNA occurred in all agrobacteria, except Agrobacterium vitis, and in most Rhizobium leguminosarum and Rhizobium etli strains but did not occur in any of the other rhizobia and bradyrhizobia studied.The structural organization of large-subunit (23S and 23S-like) rRNA molecules is known for only a limited number of bacteria (8). It has been published that in some strains of different species from a few genera, the 23S rRNA genes (rDNAs) contain in the 5Ј half highly variable extra stem-loop structures in which the cleavage and fragmentation of 23S rRNA occur (4, 6, 8-10, 12, 16, 18). Such stem-loop structures, also called intervening sequences (IVSs), and the phenomenon of 23S rRNA fragmentation have not been shown for Escherichia coli (3). Recently, the Agrobacterium 23S rRNA was also shown to be fragmented (10). In Fig. 1 the cleavage sites in 23S rRNA which were mentioned above are presented. In order to analyze the distribution of the phenomenon of 23S rRNA fragmentation in members of the family Rhizobiaceae, the rRNA patterns of 96 strains belonging to different Rhizobium, Bradyrhizobium, and Agrobacterium species were investigated (Table 1).Bacteria were grown on TY medium (1). Total RNAs were isolated from bacterial cultures at early and middle exponential growth phases by using the RNeasy Kit (Qiagen, Hilden, Germany) and analyzed electrophoretically on denaturing gels (17). Northern (RNA) transfer onto a nylon membrane (Qiagen) was done by the method of Sambrook et al. (17). The following three DNA probes were used for hybridization:

Atypical Processing in Domain III of 23S rRNA of Rhizobium leguminosarum ATCC 10004 T at a Position Homologous to an rRNA Fragmentation Site in Protozoa

“…The second processing site in 23S rRNA of R. leguminosarum ATCC 10004 T is located in the central region of the 2.6-kb rRNA fragment, in domain III of 23S rRNA. This kind of 23S rRNA fragmentation was found in most of the studied Agrobacterium strains and in many R. leguminosarum and R. etli strains (27,29). Only a fraction of the 2.6-kb rRNA fragment is processed in this region, generating two 1.3-kb rRNA fragments ( Fig.…”

“…The first one is at a position common to many ␣-proteobacterial species, in helix 9 of 23S rRNA. The helix 9 of R. leguminosarum contains an intervening sequence (IVS) (29) which is removed by RNase III cleavage (9). The 23S rRNA processing in this region leads to the occurrence of a short 5Ј rRNA fragment with a length of approximately 130 nucleotides and a 3Ј rRNA fragment with 2.6-kb length (27).…”

“…The helix 9 of R. leguminosarum contains an intervening sequence (IVS) (29) which is removed by RNase III cleavage (9). The 23S rRNA processing in this region leads to the occurrence of a short 5Ј rRNA fragment with a length of approximately 130 nucleotides and a 3Ј rRNA fragment with 2.6-kb length (27). Recently it has been shown that in Rhodopseudomonas palustris the RNase III cleavage of the IVS in helix 9 represents only an initial event of subsequent efficient processing steps leading to the removal of helix 10 and production of a 5.8S-like rRNA (34).…”

Precise characterization of rDNA genes by intraspecies and inter-loci comparison of rDNA sequences and biochemical analysis of ribosomal RNA molecules in Agrobacterium tumefaciens

“…That pioneering work was not pursued and unfortunately was not extended to enable finding of the IVS phenomena. Recently, the presence of IVS has been predicted in Agrobacterium strains (Selenska-Pobell and Evguenieva-Hackenberg, 1995;Zahn et al, 2001;Otten et al, 1996;SelenskaPobell and Doring, 1998). We conducted detailed characterization of rrns by performing intra-species comparisons and biochemical analysis of rRNA molecules in this study.…”

“…IVS was originally identified in Salmonella species (Burgin et al, 1990), and then reported in several members in g -Proteobacteria. Recently, it has been reported that IVS is also present in two a -Proteobacteria members: Brucella melitensis (Bricker, 2000) and Rhizobium species (Selenska-Pobell and Evguenieva-Hackenberg, 1995). The IVS segment is removed, and further fragmentation occurs during rRNA processing (Zahn et al, 1999;Zahn et al, 2000;Zahn et al, 2001).…”