Effects of Maturase Binding and Mg2+ Concentration on Group II Intron RNA Folding Investigated by UV Cross-Linking

The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase/maturase (LtrA protein) that promotes RNA splicing by stabilizing the catalytically active RNA structure. Here, we mapped 17 UV cross-links induced in both wild-type Ll.LtrB RNA and Ll.LtrB-Δ2486 RNA, which has a branch-point deletion that prevents splicing, and we used these cross-links to follow tertiary structure formation under different conditions in the presence or absence of the LtrA protein. Twelve of the cross-links are long-range, with six near known tertiary interaction sites in the active RNA structure. In a reaction medium containing 0.5 M NH4Cl, eight of the 17 cross-links were detected in the absence of Mg2+ or the presence of EDTA, and all were detected at 5 mM Mg2+, where efficient splicing requires the LtrA protein. The frequencies of all but four cross-links increased with increasing Mg2+ concentrations, becoming maximal between 4 and 50 mM Mg2+, where the intron is self-splicing. These findings suggest that a high Mg2+ concentration induces self-splicing by globally stabilizing tertiary structure, including key tertiary interactions that are required for catalytic activity. Significantly, the binding of the maturase under protein-dependent splicing conditions (0.5 M NH4Cl and 5 mM Mg2+) increased the frequency of only nine cross-links, seven of which are long-range, suggesting that, in contrast to a high Mg2+ concentration, LtrA promotes splicing by stabilizing critical tertiary structure interactions, while leaving other regions of the intron relatively flexible. This difference may contribute to the high rate of protein-dependent splicing, relative to the rate of self-splicing. The propensity of the intron RNA to form tertiary structure even at relatively low Mg2+ concentrations raises the possibility that the maturase functions at least in part by tertiary structure capture. Finally, an abundant central wheel cross-link, present in >50% of the molecules at 5 mM Mg2+, suggests models in which group II intron domains I and II are either coaxially stacked or aligned in parallel, bringing the 5‘-splice site together with the 3‘-splice site and catalytic core elements at JII/III. This and other cross-links provide new constraints for three-dimensional structural modeling of the group II intron catalytic core.