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Nucleic Acids Research, 2000, Vol. 28, No. 23 4623-4633
© 2000 Oxford University Press

Divergent mechanisms of 5' 23S rRNA IVS processing in the {alpha}-proteobacteria

Kenneth Zahn, Masayuki Inui and Hideaki Yukawa*

Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizu-Soraku, Kyoto 619-0292, Japan

Widespread occurrence of a separate small RNA derived from the 5'-end of 23S rRNA and of an intervening sequence (IVS) which separates this domain from the main segment of 23S rRNA in the {alpha}-proteobacteria implies that processing reactions which act to excise the IVS are also maintained in this group. We previously characterized the first example of processing of this IVS in Rhodopseudomonas palustris, which is classified with the Bradyrhizobia. In this case, IVS excision occurs by a multistep process and RNase III appears to act at an early step. Here, we characterize in vivo and in vitro IVS processing in two other related, but phenotypically distinct, Bradyrhizobia. We also examine in vivo and in vitro processing of rRNA precursors from a more distantly related {alpha}-proteobacterium, Rhodobacter sphaeroides which produces a separate 5' 23S rRNA domain but has different sequences in the 5' 23S rRNA IVS. The details of the in vivo processing of all of the Bradyrhizobial rRNAs closely resemble the R.palustris example and in vitro studies suggest that all of the Bradyrhizobia utilize RNase III in the first step of IVS cleavage. Remarkably, in vivo and in vitro studies with R.sphaeroides indicate that initial IVS cleavage uses a different mechanism. While the mechanism of IVS cleavage differs among these {alpha}-proteobacteria, in all of these cases the limits of the internal segments processed in vivo are almost identical and occur far beyond the initial cleavage sites within the IVSs. We propose that these bacteria possess common secondary maturation pathways which enable them to generate similarly processed 23S rRNA 5'- and 3'-ends.

* To whom correspondence should be addressed. Tel: +81 774 75 2308; Fax: +81 774 75 2321; Email: yukawa{at}rite.or.jp +AF23946, AF184910, AF23945


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