Intrinsic disorder in the human spliceosomal proteome

Abstract

The spliceosome is a molecular machine that performs the excision of introns from eukaryotic pre-mRNAs. This macromolecular complex comprises in human cells five RNAs and over one hundred proteins. In recent years, many spliceosomal proteins have been found to exhibit intrinsic disorder, that is to lack stable native three-dimensional structure in solution. Building on the previous body of proteomic, structural and functional data, we have carried out a systematic bioinformatics analysis of intrinsic disorder in the proteome of the human spliceosome. We discovered that almost a half of the combined sequence of proteins abundant in the spliceosome is predicted to be intrinsically disordered, at least when the individual proteins are considered in isolation. The distribution of intrinsic order and disorder throughout the spliceosome is uneven, and is related to the various functions performed by the intrinsic disorder of the spliceosomal proteins in the complex. In particular, proteins involved in the secondary functions of the spliceosome, such as mRNA recognition, intron/exon definition and spliceosomal assembly and dynamics, are more disordered than proteins directly involved in assisting splicing catalysis. Conserved disordered regions in spliceosomal proteins are evolutionarily younger and less widespread than ordered domains of essential spliceosomal proteins at the core of the spliceosome, suggesting that disordered regions were added to a preexistent ordered functional core. Finally, the spliceosomal proteome contains a much higher amount of intrinsic disorder predicted to lack secondary structure than the proteome of the ribosome, another large RNP machine. This result agrees with the currently recognized different functions of proteins in these two complexes.

Figure 1. Intrinsic disorder content of the various groups of core spliceosome proteins.

In deeper shades are marked the values for all proteins of the snRNP subunits of the major spliceosome (“snRNP proteins, major spl.”) and for all the proteins of the major spliceosome (“all proteins, major spl.”). The orange line indicates means calculated per-protein (disorder fraction was calculated for each protein first, and then a mean was taken out of this) while the green line indicates means calculated per-residue (the number of all disordered residues in a protein group divided by the total length of proteins in the group). Per-residue means are indicated above the line. Spliceosome protein groups are ordered according to per-residue means.

Figure 2. Types of disorder in core spliceosomal proteins.

Compositionally biased disorder (Y-axis) vs. disorder with SS (X-axis). Datapoints are colored according to predicted total per-residue disorder content. Groups of all proteins of the major spliceosome and all proteins of the snRNP subunits of the major spliceosome are indicated in bold.

Figure 3. Disorder in core vs. non-abundant spliceosome proteins.

Blue bars indicates values of intrinsic disorder content for core proteins, green bars for both core and additional spliceosome proteins. The blue and green lines indicate means for given protein groups, calculated per-residue. In deeper shade, values for all core (blue) and all (green) proteins associated with the major spliceosome.