Pre-mRNA splicing is a crucial step in eukaryotic gene expression and is carried out by a highly complex ribonucleoprotein assembly, the spliceosome. Many fundamental aspects of spliceosomal function, including the identity of catalytic domains, remain unknown. We show that a base-paired complex of U6 and U2 small nuclear RNAs, in the absence of the Ϸ200 other spliceosomal components, performs a two-step reaction with two short RNA oligonucleotides as substrates that results in the formation of a linear RNA product containing portions of both oligonucleotides. This reaction, which is chemically identical to splicing, is dependent on and occurs in proximity of sequences known to be critical for splicing in vivo. These results prove that the complex formed by U6 and U2 RNAs is a ribozyme and can potentially carry out RNA-based catalysis in the spliceosome.catalysis ͉ ribozymes ͉ snRNAs ͉ spliceosome ͉ U6 E xtensive mechanistic and structural similarities between spliceosomal small nuclear RNAs (snRNAs) and self-splicing group II introns (1, 2) have led to the hypothesis that the snRNAs are evolutionary descendents of group II-like introns and thus could similarly have a catalytic role in the spliceosome (3-5). However, because of the extreme complexity of the spliceosome (6-9), a dynamic cellular machine composed of more than 200 different proteins in addition to the snRNAs (U1, U2, U4, U5, and U6), it has not been possible to determine whether the snRNAs can indeed catalyze the splicing reaction without the help of spliceosomal proteins.In activated spliceosomes, U6 and U2, which are the only snRNAs required for both steps of splicing, form an extensively base-paired complex (7, 10, 11) (Fig. 1A). Considerable data support the functional importance of both the secondary and tertiary structure of the U6/U2 complex (10-13). Furthermore, an evolutionarily invariant region in U6, the ACAGAGA box ( Fig. 1 A), is in close proximity to the splice sites during splicing catalysis (14-18), and mutagenesis studies have shown that this domain plays a crucial role in catalysis of the splicing reaction (7,10,11). Two other conserved regions, the AGC triad and an asymmetric bulge in the intramolecular stemloop of U6 (ISL), are also thought to play important roles in spliceosomal catalysis (11). Recent structural studies indicate that sequences equivalent to these three regions form the active site of group II introns (19). In both systems, the ACAGAGA sequence and its equivalent in group II introns seem to be positioned in close proximity to a conserved asymmetric loop in the middle of the ISL or domain V, the corresponding stemloop in group II introns (19,20).Previously we provided evidence that in vitro-transcribed, protein-free RNAs containing the conserved central domains of human U6 and U2 could form a base-paired complex in vitro that was similar to the complex formed in activated spliceosomes (13) (Fig. 1 A). In addition, this in vitro-assembled, protein-free U6/U2 complex could catalyze a number of branching-like react...

Splicing of introns from mRNA precursors is a two-step reaction performed by the spliceosome, an immense cellular machine consisting of over 200 different proteins and five small RNAs (snRNAs). We previously demonstrated that fragments of two of these RNAs, U6 and U2, can catalyze by themselves a splicing-related reaction, involving one of the two substrates of the first step of splicing, the branch site substrate. Here we show that these same RNAs can catalyze a reaction between RNA sequences that resemble the 59 splice site and the branch site, the two reactants of the first step of splicing. The reaction is dependent on the sequence of the 59 splice site consensus sequence and the catalytically essential domains of U6, and thus it resembles the authentic splicing reaction. Our results demonstrate the ability of protein-free snRNAs to recognize the sequences involved in the first splicing step and to perform splicing-related catalysis between these two pre-mRNA-like substrates.

We have previously shown that a base-paired complex formed by two of the spliceosomal RNA components, U6 and U2 small nuclear RNAs (snRNAs), can catalyze a two-step splicing reaction that depended on an evolutionarily invariant region in U6, the ACAGAGA box. Here we further analyze this RNA-catalyzed reaction and show that while the 59 and 39 splice site substrates are juxtaposed and positioned near the ACAGAGA sequence in U6, the role of the snRNAs in the reaction is beyond mere juxtaposition of the substrates and likely involves the formation of a sophisticated active site. Interestingly, the snRNA-catalyzed reaction is metal dependent, as is the case with other known splicing RNA enzymes, and terbium(III) cleavage reactions indicate metal binding by the U6/U2 complex within the evolutionarily conserved regions of U6. The above results, combined with the structural similarities between U6 and catalytically critical domains in group II self-splicing introns, suggest that the base-paired complex of U6 and U2 snRNAs is a vestigial ribozyme and a likely descendant of a group II-like self-splicing intron.

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