The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine

Abstract

Almost all primary transcripts in higher eukaryotes undergo several splicing events and alternative splicing is a major factor in generating proteomic diversity. Thus, the spliceosome, the ribonucleoprotein assembly that performs splicing, is a highly critical cellular machine and as expected, a very complex one. Indeed, the spliceosome is one of the largest, if not the largest, molecular machine in the cell with over 150 different components in human. A large fraction of the spliceosomal proteome is organized into small nuclear ribonucleoprotein particles by associating with one of the small nuclear RNAs, and the function of many spliceosomal proteins revolve around their association or interaction with the spliceosomal RNAs or the substrate pre-messenger RNAs. In addition to the complex web of protein-RNA interactions, an equally complex network of protein-protein interactions exists in the spliceosome, which includes a number of large, conserved proteins with critical functions in the spliceosomal catalytic core. These include the largest conserved nuclear protein, Prp8, which plays a critical role in spliceosomal function in a hitherto unknown manner. Taken together, the large spliceosomal proteome and its dynamic nature has made it a highly challenging system to study, and at the same time, provides an exciting example of the evolution of a proteome around a backbone of primordial RNAs likely dating from the RNA World.

Fig. 1. Schematic representation of a group II self-splicing intron, from which spliceosomes may have evolved

The exons are shown in gray rectangles. The identity of each RNA domain is indicated close to each domain. The sites of 5′ and 3′ splice sites and branch site are marked as 5′SS, 3′SS and BS, respectively. The functional and/or structural homologue of each RNA element in the spliceosome is shown in gray circles.

Fig. 2. The interaction of U6, U5 and U2 snRNAs with the pre-mRNA before the first step of splicing

The basepairing interactions within each snRNA, between U6 and U2 snRNAs and between snRNAs and the pre-mRNA are shown. Numbers reflect the human numbering system. The exons in pre-mRNA are shown as solid rectangles, with the intron shown as a line. The sequence of the 5′ splice site and branch site are shown.

Fig. 3. The RNA and protein composition of each snRNP particle

Note that all snRNPs except U6 carry a set of Sm proteins, whereas U6 instead contains LSm proteins.

Fig. 4. The spliceosomal cycle

The pre-mRNA is shown in black, and the location of the branch site is marked by an A. The exons are shown as solid rectangles and the intron is drawn as a thin line. The spliceosomal complexes and snRNPs are shown in gray. The identity of each spliceosomal complex and snRNP particle is shown. The main steps of spliceosomal cycle, assembly, catalysis, disassembly and recycling are marked on the graph. The main proofreading steps of spliceosomal cycle are marked by clock signs and the main RNA helicases involved in each conformational rearrangement are indicated. The snRNAs within each spliceosomal complex are shown.