Biology Reference
In-Depth Information
the spliceosomal assembly pathway, are themselves alternatively spliced, hence may occur in several
isoforms. For example, the U2 snRNP specific component SF3b14 shows five predicted alternative
splice forms of different types (source ASD [Thanaraj
et al.
, 2004]). The interactions of SF3b14
are well described [Spadaccini
et al.
, 2006], including the location of functional domains within the
protein sequence. Since more and more spliceosomal factors are described in such detail, it should be
possible in the near future to estimate the impact of alternative splicing on the spliceosome, which poses
an interesting example of combinatorial complexity. Suppose that in the four stages of spliceosome
assembly only one protein factor occurs in two functionally different isoforms, then about 2
4
=
16
different spliceosomes could be assembled and contribute to different alternative splicing decisions
(neglecting that some alternative splice forms do not reach the protein level). This is a rough estimate of
the lower boundary as many more spliceosomal proteins exist, and most of their genes are likely to be
alternatively spliced.
The network of spliceosomal assembly as presented here, serves as a basic scaffold to successively
map the occurrence and impact of alternative splice events on the assembly pathway. This can lead
to interesting hypotheses about which alternative splice event contributes to which spliceosomal state,
making spliceosomes classifiable and probably even attributable to specific splicing patterns. For
example, if the ability to become phosphorylated of an SR protein splicing factor, like ASF/SF2, is
impaired due to alternative splicing, this will influence its contribution to splice site recognition. As
consequence the spliceosome will possibly fail to recognize weak splice sites under this condition.
Additionally, since other splicing factors for example, SC35 or TIA1 influence E-complex assembly,
redundancy in recognition of pre-mRNA signals by interchangeable factors must be taken into account.
Concerning the presented Petri net modeling approach, we can summarize the following achievements:
1. Translation of different lines of evidence for modular subsystems of the spliceosomal assembly
pathway from experimental literature into a unique mathematical formalism.
2. Compilation of T-Invariants (P-invariants) based on the commonly applied steady state assumption
for biochemical networks. Assignment of a biological meaning to each T-invariant (P-invariant).
3. Model validation resulting in a network completely covered by T-invariants.
4. Representation of combined partial pathways, each supported by experimental reports, allowing
for model expansion and testing of new hypotheses.
5. Inclusion of special aspects of 5' splice site recognition during E-complex formation as well as the
potential activation of a discard pathway as simplified model for a kinetic proofreading mechanism
during C-complex formation.
6. Easier identification of discrepancies in current experimental data by the combinatorial arrangement
of the subpathways. For example, the activation of UAP56 by U2AF stands in contradiction to
the apparent requirement of UAP56 for transition from the E-complex to the A-complex within the
U2AF independent A-complex assembly pathway.
7. Comprehensive and condensed visualization of the spliceosomal assembly process, allowing the
global inspection of similar and distinct routes. This facilitates the apprehension of a large network
such as the spliceosomal assembly pathway and its further extension.
The clustering of T-invariants, representing signaling pathways and participating in spliceosome forma-
tion, indicates that there exists a variety of similar pathways leading to the same intermediate complexes.
Although each T-invariant, describing one of these routes, is minimal in that it would fail with the loss of
one reaction, it is clearly visible that there exists a redundancy in routes leading to the formation of inter-
mediate states. This observation provides the interesting aspect of a backup failure mechanism, ensuring
