Biology Reference
In-Depth Information
Table 1
Exemplary description of T-invariants i13 and i14, describing signaling pathways during the process of
spliceosome assembly
ID #t Biological Interpretation
13 91 U1 independent 50ss activation, early SF3b125 action (t13.17S U2 matur2) in U2 maturation
14 92 As i13, but via late SF3b125 action (t22.17S U2 matur1) in U2 snRNP maturation
The complete table of all T-Invariants is given in the supplemental material.
This results in seven places, describing the tri-snRNP and B-complex formation, which form a P-
invariant for conservation of Prp31 in the system. The fact that Prp31 is required for successive rounds
of tri-snRNP and spliceosome formation suggests this protein to be abundantly available, which in
turn justifies a conservation relation. Furthermore, Prp31 is a crucial factor in spliceosome assembly,
because mutations in its gene are related to the blindness causing disease
retinitis pigmentosa
[Schaffert
et al.
, 2004]. Since all T-invariants, involving the reaction
t47.U4 U6 bdg
(approximately 79% of all
T-invariants) can only fire in the presence of Prp31, the model demonstrates that more than three quarter
of the network would fail if this protein would be knocked out.
Prp38 (yeast ortholog of human protein 27K) forms a similar albeit smaller P-invariant of five places,
which, except for Prp38, is itself a complete subset of the Prp31 P-invariant. The time of appearance and
release of Prp38 is less clear, but it was shown to associate with higher affinity (and thus stability) with
the assembled U4/U6 U5 tri-snRNP than with an individual U snRNP [Xie
et al.
, 1998]. Hence, it was
modeled to enter tri-snRNP formation at the time of U5 snRNP integration. Its involvement in structural
rearrangement of the U4/U6 complex without possessing a DExD/H domain to actively participate in
the required hydrolyzation reactions, makes it a putative auxiliary factor for the DExD/H box helicase
Prp28 [Xie
et al.
, 1998; Lybarger
et al.
, 1999]. The possible connection between Prp38 and the helicase
Prp28, which catalyzes the unwinding of the U4/U6 snRNA duplex upon U2 snRNP integration [Xie
et
al.
, 1998], implies that both proteins exit from the active assembly pathway after this step. In this way,
Prp38 might as well as Prp31 form a conservation relation at the stage of B-complex formation.
The fourth P-invariant defines the cycling of the DExD/H box helicase, Prp16, which is a crucial
determinant of the second catalytic step, by catalyzing the initial conformational changes in transition
from the first to the second catalytic step [Staley and Guthrie, 1998]. Prp16 binds transiently, being no
integral snRNP component, and leaves the spliceosome upon ATP hydrolyzation [Schwer and Guthrie,
1991]. This P-invariant consists only of three places (including free Prp16), denoting the intermediate
complexes
p90.U2 5ss U6 U5 conf1
and
p100.U2 5ss U6 U5 conf2
, in which Prp16 unfolds its cat-
alytic activity. In contrast to other helicases involved in structural rearrangements (
e.g.
, Prp28), this
enzyme occurs not in different branches, and, thus, explaining its appearance in a conservation relation.
In general, the appearance of essential enzymes in conservation relations can be meaningful to reflect
their availability for subsequent cycles of spliceosome assembly, which may require a constant presence
proximal to the location of spliceosome formation. The identified P-invariants suggests that more
spliceosomal factors exists whose relative concentration do not change markedly via repeated cycles of
spliceosome assembly. Lack of evidence at which time other catalytically active proteins specifically
(re)enter the assembly process or how long they remain associated with the main complex, presently limit
the modeling of further P-invariants. Note that in contrast to metabolic networks, where commonly only
low molecular substances appear in conservation relations, here also enzymes or intermediate complexes
can be conserved within a defined signaling network.
